Tag: CP2K

Umbrella Sampling using Cp2k

Dear all, I’m trying to carry out umbrella sampling for a dimeric system. My collective variable is center of mass to center of mass distance. The COLVAR and CONSTRAINT section is as follows. I’m getting different error with different modifications. Can anyone suggest me how to correct it ? Thanks…

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Molecular Dynamics Software Market to Witness Revolutionary

Molecular Dynamics Software Market Global “Molecular Dynamics Software Market” Research report is an in-depth study of the market Analysis. Along with the most recent patterns and figures that uncovers a wide examination of the market offer. This report provides exhaustive coverage on geographical segmentation, latest demand scope, growth rate analysis…

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Debian — Details of package cp2k in bookworm

Ab Initio Molecular Dynamics CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics (AIMD) simulations. CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method…

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Breaking a ligand with umbrella sampling – User discussions

ryanm January 19, 2024, 6:40pm 1 GROMACS version: 2022GROMACS modification: YesHere post your questionCan GROMACS umbrella sampling break two bonded atoms in a ligand? Example: using umbrella sampling to show the maximum force to break the carbon and oxygen bond in carbon dioxide molecule. Bonds cannot break or form in…

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periodic HF with TC-LRC in a non-orthogonal cell

Dear CP2K experts, I started a single-point energy calculation with the PBE0 functional using the TC-LRC and ADMM techniques. I have set      CUTOFF_RADIUS  5.8 in both  PBE_HOLE_T_C_LR  and  INTERACTION_POTENTIAL sections. My cell is specified by     &CELL      A     11.8510781995796848      0.0000000000000000  …

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CP2K QMMM Calculation seems to randomly crash

Dear all, I have encountered a very disturbing phenomena.  My system is fairly simple: One Na+ in water (up to 800 water molecules). I generated the system using tleap. The plan is the following: Since full semi empirical MD with XTB is costly for 801 atoms, I tried to calculate…

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metadynamics restart: CHOLESKY

Dear developers and users: I wish to ask what to do,  if using a restart file from a previous metadynamic run  (updated to inp extension: please, see the attached) CP2K terminates with a notice Cholesky decompose failed: the matrix is not positive definite or * *    |      …

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A Comprehensive Overview for the 2024-2031 Period| With 117 Pages

PRESS RELEASE Published December 12, 2023 Latest Research Report On “Molecular Dynamics Simulation Software Market” 2024 Analysis, Future Projection, Forecast By 2031 | With {117} Pages Global “Molecular Dynamics Simulation Software Market” Research Report 2024-2031 is a factual overview and in-depth study of the current and future market of the Molecular…

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Molecular Dynamics Simulation Software Market Worth Observing Strong Growth by Abalone, Software for Chemistry and Materials (SCM), Ascalaph Designer

The Molecular Dynamics Simulation Software Market research report provides all the information related to the industry. It gives the market’s outlook by giving authentic data to its client which helps to make essential decisions.  It gives an overview of the market which includes its definition, applications and developments, and manufacturing…

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Molecular Dynamics Software Market Comprehensive Analysis by Abalone, Software for Chemistry and Materials (SCM), Ascalaph Designer

A2Z Market Research recently published its latest research study on the Global Molecular Dynamics Software Market, comprising over 130+ pages of analysis on the business strategies adopted by both key and emerging industry players. The report provides insights into the current market development, landscape, technologies, drivers, opportunities, market outlook, and…

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Molecular Dynamics Software Market Analysis, Future Demand, and Global Industry Forecast to 2030 |Abalone, Software for Chemistry & Materials (SCM), Ascalaph Designer, Avizo (Software), CHARMM

A2Z Market Research has published a report that represents the process of collecting, analyzing, and interpreting data about a Molecular Dynamics Software market. This is a crucial step in developing a business strategy or launching a new product, as it helps companies to gain a deeper understanding of the Molecular…

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MOF optimization

Hi a few general remarks: For the use of hybrid functionals in PBC, you should use an interaction potential with a cutoff (6 Angstrom should be ok). Make sure that you have enough memory to keep the integrals in core (print HF_INFO, set MEMORY). EPS_SCHWARZ can most likely be set to 1.E-08. …

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Significant discontinuity in EOS curver for FeO

Dear CP2K community, I am calculating the EOS for FeO with a 2*2*2 supercell. But there is always a significant discontinuity (sharp decrease) in the range of 4.3-4.4 angstrom lattice constant in the EOS curves, as shown in the figures below. I have done the following tests:– the convergence of…

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Problem with GW core electron calculations

Dear CP2K users   I try to calculate core binding energies using GW calculations. I am interested in the Cl2p line of a Cl- ion on the top of Mg*6H2O crystal:  I performed a first-principle MD, and due to the computational/ memory cost of the calculations, I extracted different snapshots…

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Problem when combining coordination numbers as one collective variable

Dear CP2K developers,    I’m trying to use the &COMBINE_COLVAR section in CP2K (version 2022.1) to combine two coordination numbers as one collective variable (CV), and output the Lagrange multipliers of this CV. However, I encounter problems in both the AIMD simulation and the Lagrange multipliers. I update an input…

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SCCS is not yet implemented with GAPW?

Dear cp2k developers, I am trying to use Andreussi’s method with the all-electron GAPW method. According to the manual, SCCS is not yet implemented with GAPW.  So it is not surprising that the calculation fails with an error message  “SCCS is not yet implemented with GAPW”  However, when I change…

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Nvidia announces H200, designed to handle AI work better, How better is it than the H100? Know here

Nvidia H200: Leading chip manufacturer Nvidia has released the H200, a top-of-the-line chipset designed for AI applications. With numerous large firms, including Amazon Web Services, Google Cloud, Microsoft Azure, and Oracle Cloud Infrastructure, already pledging to utilise the chipset next year, the upgrade to the already well-liked H100 chipset will begin…

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Nvidia’s H200 GPU To One-Up H100 With 141GB Of HBM3e As Memory Race Heats Up

Components & Peripherals News Dylan Martin November 13, 2023, 09:00 AM EST The H200 features 141GB of HBM3e and a 4.8 TB/s memory bandwidth, a substantial step up from Nvidia’s flagship H100 data center GPU. ‘The integration of faster and more extensive memory will dramatically improve…

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Deploy CP2K on an Azure virtual machine

This article describes the steps for running a CP2K application on a virtual machine (VM) deployed on Azure. It also presents the performance results of running CP2K on single-node and multi-node VM configurations. CP2K is a quantum chemistry and solid-state physics software package that can perform atomistic simulations of solid…

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Accepted cp2k 2023.2-2 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 13 Nov 2023 02:52:52 -0500 Source: cp2k Architecture: source Version: 2023.2-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Andrius Merkys <mer…@debian.org> Changes: cp2k (2023.2-2) unstable; urgency=medium . * Team upload. * No-changes source-only upload to rebuild with libsymspg2….

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Multiples WALKERS

Hi Nacho, I’m running a multiple walkers MTD with CP2K and PLUMED as well. As far as I know, you must create a folder where the HILLS files of all walkers will be stored together. This folder is external to the those where the walkers’ dynamics is stored….

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DFTB for CP2K with Gromacs – User discussions

caspar November 8, 2023, 12:28pm 1 GROMACS version: AnyGROMACS modification: NoHello, I am interested in running QM/MM calculations using the CP2K interface. In the manual it states that (so far) BLYP and PBE are supported, however, later the inclusion of further methods including DFTB is suggested. Does a timeline exists,…

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QM/MM – Gromacs+CP2K ERROR – User discussions

(last update version) Hello all, I am trying to apply QM/MM with Gromacs+CP2K interface but I have an error… I have Gallium and basic, N,O,H,C atoms. CP2K part is giving error. during energy minimization part. Probably gromacs part has a problem as well… I am sharing with you my input…

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Phase Fixing in TD-DFPT Calculation

Dear CP2K Developers, I would have a question concerning the fixing of the phase of the molecular orbitals in CP2K in general, but especially in the TD-DFPT module. The TD-DFPT Module prints the singlet excited states in terms of weighted elementary particle-hole excitation’s between the occupied and virtual (DFT) molecular…

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CP2K v2023.2 – Spin-Orbit Coupling Calculation

Dear developers, I’d like to express my gratitude for your ongoing efforts in developing and updating CP2K. I recently tried out the latest version, CP2K v2023.2, and noticed the addition of a new pseudopotential file ‘GTH_SOC_POTENTIALS’ in the `data` folder. I’d like to perform PDOS calculations with spin-orbit coupling (SOC)….

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19464] Computing MO coefficients using CP2K outputs

Hi, For educational purposes, I wanted to show how CP2K generates the MO coefficients. I’ve selected benzene with a SZV basis and the convergence limit is `1.0e-8`. Then, I printed the overlap (S), Kohn-Sham (K), and density matrices (P) in my input (using `&AO_MATRICES` section) and parsed them into Python….

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Molecular Dynamics Software Market Is Booming Worldwide

Report Description: Global Market Vision has rolled out a new report namely Molecular Dynamics Software Market that integrates crucial insights on the market. The report supplies a comprehensive analysis of business aspects like market size, competitive scenario, market opportunities, market shares, and revenue growth patterns, and the volume and value…

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Basis Set in Periodic Calculation

Hi CP2K Developers, I am currently working on a python3 tool to compute non-adiabatic coupling constants from the CP2K printed Kohn-Sham Hamiltonian and the Overlap Matrices (OLM). To compute this, I have to compute the basis transformation matrix between the atom centered basis at say a geometry 1 and another…

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units of psi^2

hi everyone! I am using the cp2k implementation to calculate hyperfine tensors. no problems here so far, i got some results using an all-electron basis set. now, unfortunately, i cannot find any information on how this is done internally and also i cannot assign the units. e.g. in which units…

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no longer buildable on armel

Source: cp2k Version: 2023.1-2 Severity: serious Control: close -1 2023.2-1 Tags: sid trixie User: release.debian….@packages.debian.org Usertags: out-of-sync Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 30 days as having a Release Critical bug in testing [1]. Your package src:cp2k has been…

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Help with running cp2k in parallel with Slurm

Dear all, I am trying to run cp2k on our HPC cluster and I am new in doing any kind of parallel computing and work on a cluster, so I would appreciate if some help and I apologize if I am missing something obvious. I have a .sif file in…

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cp2k 2-4 installation and regresstio test result

Hi, I am new to the CP2K and learning the program.  I downloaded the program last week and tried to install it on our computer,after several attempts with intel (version 12) and gfortran (4.6), I found that the regression test with Linux-x86-64-gfortran.popt failed only 22 cases (using mpiexec -np 2…

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Bioinformatics Software Market to Witness Robust Expansion by 2030

The Bioinformatics Software Market research report provides all the information related to the industry. It gives the market’s outlook by giving authentic data to its client which helps to make essential decisions.  It gives an overview of the market which includes its definition, applications and developments, and manufacturing technology. This…

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Ehrenfest + Field problem for version 2023.2

Dear CP2K community, On 24 February 2023 I made some changes in the Real-Time calculation part of the code which turned out to break one specific behavior: Ehrenfest Dynamics with a time-dependent field. This has been fixed the 9 October 2023. Thus, if you are using Ehrenfest Dynamics with a…

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Extracting Atomic Forces from XYZ Trajectories in CP2K

Dear CP2K Community, We have encountered a challenge while working with MD trajectories in XYZ format. Specifically, we have trajectories containing atomic positions and velocities for each frame, but unfortunately, we do not have the corresponding atomic forces. In theory, it is possible to calculate atomic forces based on atomic…

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Install cp2k with cuda in a geforce gtx 1650 card

Hello,  I am trying to install cp2k with cuda enable in a  geforce gtx 1650 card, but in the gpu-ver –gpu-ver                 Selects the GPU architecture for which to compile. Available                          …

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CP2K Research Scientist/Software Developer at CASUS

The position will be based in Görlitz with a postdoctoral/senior scientist full-time contract and the possibility for a permanent position.  Potential candidates must have a PhD degree in Chemistry, Physics, or related discipline and a strong interest in computer simulations,  as well as programming. Demonstrable experiences with Linux, version control using git, electronic structure…

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Is is possible to output Fe1 (spin up) and Fe2 (spin down) information in the -pos-1.xyz file

Dear Colleagues, I am currently doing AIMD simulation for FeO system using CP2K. In the input file, it is common practice to set two types of Fe atoms, Fe1 (spin up) and Fe2 (spin down).  But in the output file, Fe1 and Fe2 are not distinguished, as shown in the…

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Band gap-HSE06-UiO-66

Hi I assume the difference is due to basis sets. Plane waves usually describe conduction band states better than localized orbitals. So increase the primary basis. Important: if you are using a new version of CP2K, you should not set EPS_PGF_ORB. -> www.cp2k.org/faq:hfx_eps_warning Since version 2023.2 The occupancy of the Kohn-Sham matrix…

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Mdrun : An error occurred in MPI_Allreduce – User discussions

AKA October 1, 2023, 9:58pm 1 GROMACS version: 2022.6GROMACS modification: No I am running gromacs-cp2k and I get the following error when running mdrun on qmmm system. 🙂 GROMACS – gmx mdrun, 2022.6 (-: Executable: /usr/local/gromacs-cp2k-gpu/bin/gmx_mpi Data prefix: /usr/local/gromacs-cp2k-gpu Working dir: /home/vivek/Desktop/cp2k_test/tutorial/egfp Command line: gmx_mpi mdrun -s egfp-qmmm-nvt.tpr -deffnm egfp-qmmm-nvt…

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CUDA enabled Gromacs Cp2k installation error – User discussions

AKA September 27, 2023, 2:02pm 1 GROMACS version:2023.2GROMACS modification: NoCP2K version: 2023.2Hello all,I was trying to install gromacs with cp2k on nvidia GPU. I installed the psmp version of “local_cuda” cp2k. The cmake command I used is present is: cmake .. -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_GPU=CUDA -DGMX_CP2K=ON -DCP2K_DIR=/home/aka/Documents/cp2k-2023.2/lib/local_cuda/psmp -DCMAKE_PREFIX_PATH=’/home/aka/Documents/cp2k-2023.2/tools/toolchain/install/openblas-0.3.23;/home/aka/Documents/cp2k-2023.2/tools/toolchain/install/scalapack-2.2.1′ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-cp2k-gpu/…

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Molecular Dynamics Simulation Software Market Size, Share 2023 To 2030 | Abalone, Software for Chemistry & Materials (SCM), Ascalaph Designer

The global Molecular Dynamics Simulation Software market is expected to grow at a CAGR of 12.4% from 2023 to 2030. The Molecular Dynamics Simulation Software market research report is a comprehensive and authoritative source of information on the market. It provides businesses with the insights they need to make informed…

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Non-zero exit code detected

Dear Hongyang, www.cp2k.org/faq:toolchain_non_zero_exit_code_detected (just created based on your screenshot) Since you’re providing an up-to-date compiler (I assume you also have gfortran from the gcc 9.1.0 suite) and openmpi yourself, there is usually no need to use “–install-all” for the toolchain script. Hope this helps, best regards, Tiziano Am 22.06.19 um 14:07 schrieb Hongyang Ma: >…

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On the time&memory consumption of ERI calculation in CP2K hybrid functional single point

Dear CP2K team, I am attempting to calculate the single point energy of a huge periodic cluster (near 5k atoms, just contains C H O N, cell size 30+ angstrom, only Gamma point). Due to the demand of following analysis, I used B3LYP hybrid functional (with D3(BJ)) and 6-31G(d)…

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Bioinformatics Software Market Size, Growth | Global Report [2023-2030]

Introducing Our Latest Bioinformatics Software Market Research Report Unveiling In-Depth Analysis of Industry Trends, Growth, and Opportunities: The Bioinformatics Software Market 2023-2030 | research report provides a detailed analysis of the market’s various types [Knowledge Management Tools, Bioinformatics Platforms, Bioinformatics Services] and applications [Medical bioinformatics, Animal bioinformatics, Agricultural bioinformatics, Scholars…

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How do Atoms Move in an Electric Potential

Hi All, I had a theoretical question regarding the electric potential that is applied in CP2K. Let’s say that a simulation box has a electric potential gradient applied to it in the +x-direction: electric potential gradient = 2X If you have positively charged ions (cations) and negatively charged ions (anions),…

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CP2K version 2023.2 compile error

Thank you for helping me, Mishra. However, I still got problems. I modified the script according to my architecture, as below:“spack -d install cp2k@2023.1+elpa %g…@8.3.1 target=icelake ^elpa+openmp ^ope…@4.1.4 fabrics=auto”Then I got very, very long error message below and I dont’ know what is the reason. ———————————————————————————————————————————————————————————– ==> [2023-09-22-11:22:05.969419] Error: ProcessError:…

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Read the coefficients for the wave function from WFN files, and combine them

Hi Daniele, I once wrote a parser for the molecular orbital coefficients in Python: github.com/ondrejkrejci/PPSTM/blob/master/pyPPSTM/ReadSTM.py#L520 You can obtain the MO file like this: &DFT &PRINT &MO ON EIGVECS CARTESIAN FILENAME cartesian-mos &EACH QS_SCF 0 &END EACH &END MO &END PRINT &END DFT -Ole On 2018-09-27 10:09, Daniele Ongari wrote: > Thank you for the hint, but I think something is going weir…

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Gromacs +cp2k installation – User discussions

GROMACS version: 2023.1 Hello. I am trying to compile gromacs-2023.1 with cp2k-2023.2, but I am not being able to link the fftwf3 library. So when I run the following command: cmake … -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_DOUBLE=ON -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/home/edivaldo/cp2k/tools/toolchain/install/fftw-3.3.10/lib -DFFTWF_INCLUDE_DIR=/home/edivaldo/cp2k/tools/toolchain/install/fftw-3.3.10/include -DGMX_BLAS_USER=/home/edivaldo/cp2k/tools/toolchain/install/openblas-0.3.23/lib/libopenblas.a -DGMX_LAPACK_USER=/home/edivaldo/cp2k/tools/toolchain/install/scalapack-2.2.1/lib/libscalapack.a -DGMX_CP2K=ON -DCP2K_DIR=“/home/edivaldo/cp2k/lib/local/psmp” -DGMX_MPI=on I keep getting this warning:– The…

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gromacs23.2+Cp2k23.2 installation error – User discussions

AKA September 19, 2023, 8:04am 1 GROMACS version: 2023.2GROMACS modification: NoHello. I am trying to compile gromacs 2023.2 with cp2k 2023.2 support. I am facing the following error while running make: lto1: fatal error: multiple prevailing defs for ‘__def_init_helium_types_Density_properties_type’ compilation terminated. lto-wrapper: fatal error: /home/aka/Documents/cp2k-2023.2/tools/toolchain/install/gcc-13.1.0/bin/g++ returned 1 exit status compilation…

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Bioinformatics Software Market Landscape: Trends, Innovations, and Top Players Strategic Outlook 2030

“Bioinformatics Software Market” Size, Share, Growth Report 2023-2030 | No. of Pages: 105 | Report which offers an in-depth analysis Grounded on Applications (Medical bioinformatics, Animal bioinformatics, Agricultural bioinformatics, Scholars and microbial genomes), and Types (Knowledge Management Tools, Bioinformatics Platforms, Bioinformatics Services) and expected to Grow Annually By Magnificent (CAGR…

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Global Bioinformatics Software Market Size, Growth | Global Report [2023-2031]

Global “Bioinformatics Software Market” offers a detailed Report of |111 Pages| which is expected to witness remarkable growth in the coming years. The implementation of new technologies and innovative solutions will drive the market’s revenue generation and increase its market share by 2031 with Revenue by Type (Knowledge Management Tools,…

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Bioinformatics Software Market will reach USD Million 2030 (New Report) by Business Insights, Top Companies, consumption by Regional data

Bioinformatics Software Market (CAGR 2023 – 2030) |No. of pages: [105] | market size, share, and industry analysis, By Type [, Knowledge Management Tools, Bioinformatics Platforms, Bioinformatics Services, ,], Application [, Medical bioinformatics, Animal bioinformatics, Agricultural bioinformatics, Scholars and microbial genomes,], and regionhas seen significant growth and advancement due to…

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Accepted cp2k 2023.2-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sat, 16 Sep 2023 18:44:06 +0530 Source: cp2k Architecture: source Version: 2023.2-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Michael Banck <mba…@debian.org> Changes: cp2k (2023.2-1) unstable; urgency=medium . * New upstream release, new features include: + Intrinsic Atomic Orbitals…

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How to install cp2k on Ubuntu

Install cp2k Installing cp2k package on Ubuntu is as easy as running the following command on terminal: sudo apt-get update sudo apt-get install cp2k cp2k package information More information about install using apt-get Advanced Package Tool, or APT, is a free software user interface that works with core libraries to…

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Dcd file and VMD

Dear Cp2k developers, I use FIST on Cp2k version 2.0.0, with a system in a monoclinic cell that I specify by giving the three vectors A,B and C. Indeed, in the output I get INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.1199999E+03 The corresponding .dcd file contains in the array cell(6) only the diagonal part of…

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Using .molden File as a Restart File in CP2K

Dear CP2K Community, I am currently attempting to use a .molden file as the Restart file for SCF_GUESS in CP2K, but I have encountered a “nspin is not equal” warning and a subsequent “Reducing nspin is not possible” error. To provide additional context, I have attached both the input and…

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Bioinformatics Software Market Research | 2023-2030

The Bioinformatics Software Market Insights of 2023 is an extensive and comprehensive report that provides a complete analysis of the market’s size, shares, revenues, various segments, drivers, trends, growth, and development. The report also highlights the limiting factors and regional industrial presence that may affect the market’s growth trends beyond…

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2030, Molecular Dynamics Simulation Software Market Size and Share Analysis

PRESS RELEASE Published September 11, 2023 Pre and Post Covid Report Is Covered | Final Report Will Add the Analysis of the Impact of Russia-Ukraine War and COVID-19 on This Industry. [117 Pages Report] “Molecular Dynamics Simulation Software Market” size is projected to reach Multimillion USD by 2030, In comparison…

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Molecular Dynamics Simulation Software Market 2023 Growth with Trends and Scope

Global “Molecular Dynamics Simulation Software Market” offers a detailed Report of |109 Pages| which is expected to witness remarkable growth in the coming years. The implementation of new technologies and innovative solutions will drive the market’s revenue generation and increase its market share by 2030 with Revenue by Type (Chemical…

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Assistance and clarifications with NEGF Module

Hello everyone, I am attempting to use the NEGF implementation in CP2K for transport calculations. At present I have a monolayer between two aluminum [110] contacts (details not too important as it is just a test case). I have been using the examples provided online here from Dr. Chulkov as my…

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Grace is twice as efficient as AMD and Intel processors

Grace is Nvidia’s next new processor for supercomputers and data centers. Unlike competitors AMD and Intel, Nvidia is based on the ARM architecture and not x86-64, which makes the performance comparisons particularly interesting. Now Nvidia itself has published the results of a series of comparative performance tests, with the Grace…

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Minima hopping problems

Hello,  I am new to minima hopping and I have a few questions. I already tried google and this forum, but nothing helped. I tried with FORCE_EVAL > METHOD > FIST but all I get is an astronomical Worker’s / MD temperature in the output and an exploded system in…

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Problem with the calculation of the CUBE file and Wannier Centres using the ROKS method?

Dear colleagues,  Could you please help me to understand the CP2K implementation of ROKS and the Wannier Centers. I am facing the following two problems. I can’t find an answer in the documentation. And, unfortunately, I don’t really understand in the code. 1) The ROKS implementation in CP2K uses a …

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Non-Periodic system WARNINGS.

Dear all,  I want to run a AIMD calculation in cp2k. I have prepared a box using packmol consisting of my system and 104 water molecules with cubic size of 15.1 x 15.1 x 15.1. And I want the my system to be in the center. It is a non-periodic…

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Signal 11 segmentation fault met with popt in cp2k-8.2

Dear all, I’m a beginner. I just finished compiling cp2k and met an error while running cp2k.popt for the first time with command ‘mpirun -np 4 cp2k.popt ./test.inp’ (Blue characters below are the full output) Primary job  terminated normally, but 1 process returneda non-zero exit code. Per user-direction, the job…

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Global Aerosol Packaging Market [2023]

The Global Aerosol Packaging Market Size Reached USD 3489.43 Million in 2021. It is Expected to Grow at a CAGR of 10.13%. The Global Aerosol Packaging Market to Reach the Value of USD 6225.66 Million During Forecast Period. Revolutionary New Findings Uncovered in the Latest Report. Get a Sample PDF…

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Question on TRPMD

Dear all, I would like to explore TRPMD in CP2K, by running low-temperature TR-PIMD simulations for a small molecular crystal, say some small amino acid.  I have few questions: is it possible to run TRPMD and then extract VDOSes from autocorrelation function of the centroid? Can I use it then…

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Problem with small molecule MM

Dear CP2K users, I am trying to run a MM geometry optimization for a small molecule using CP2K. I have prepared the pdb and psf files for the molecule using Charmm-Gui and I am using the cgenff forcefield. For some reason, I am getting this strange error:  A string type…

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2D Ewald summation in CP2K

Dear CP2K Developers and Users, I am writing to check if the 2D Ewald summation is available in CP2K. This would be a preferred methods for a liquid system with ions (or completely ionic melt) that my develop a significant curvature at the liquid-vacuum interface. If this happens, the approach…

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How to recalculate the total energies from KS eigenvalues

of NO on an Au(111) slab using CP2K. During the standard GPW  calculation, I receive the following components of the total energy: Overlap energy of core charge distribution  Self-energy of the core charge distribution  Core Hamiltonian energy  Hartree energy  Exchange-correlation energy While summing up these components will give me the…

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Molecular Dynamics Software Market 2023-2031- Abalone, Software for Chemistry & Materials (SCM), Ascalaph Designer, Avizo (Software), CHARMM

Molecular Dynamics Software Market Report Coverage: Key Growth Factors & Challenges, Segmentation & Regional Outlook, Top Industry Trends & Opportunities, Competition Analysis, COVID-19 Impact Analysis & Projected Recovery, and Market Sizing & Forecast. Latest launched research on Global Molecular Dynamics Software Market, it provides detailed analysis with presentable graphs, charts and tables….

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cp2k 2023.2 – Download, Browsing & More

cp2k 2023.2 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of cp2k-2023.2.tar.bz2 (27 Jul 10:02, 68243435 Bytes) About: CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material,…

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ARCHER2 Weekly Newsletter

By ARCHER2 Service on July 26, 2023 Tags: newsletters 

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Bioinformatics Software Market: Latest Innovations 2023

PRESS RELEASE Published July 25, 2023 Latest Bioinformatics Software Market Dynamics and Innovations 2023: Market Segmentation by Types [Knowledge Management Tools, Bioinformatics Platforms, Bioinformatics Services], and Applications [Medical bioinformatics, Animal bioinformatics, Agricultural bioinformatics, Scholars and microbial genomes] with Growing CAGR. The Bioinformatics Software market has witnessed growth from USD million…

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Gromacs installation with cp2k – User discussions

vikas July 25, 2023, 12:40pm 1 GROMACS version: 2021.4GROMACS modification: NoBelow is the cmake command I am using:cmake … -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_DOUBLE=ON -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=$cp2k_install/fftw-3.3.10/lib/ -DFFTWF_INCLUDE_DIR=$cp2k_install/fftw-3.3.10/include -DGMX_BLAS_USER=$cp2k_install/openblas-0.3.20/lib/ -DGMX_LAPACK_USER=$cp2k_install/scalapack-2.1.0/lib/ -DGMX_CP2K=ON -DCP2K_DIR=$cp2k_home/lib/local/psmp/ -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_cp2k -DGMX_LIBS_SUFFIX=_cp2k -DCMAKE_INSTALL_PREFIX=/home/chemistry/phd/cyz208667/Softwares/new_cp2k/gmx_install -DCP2K_LINKER_FLAGS=“-Wl,–enable-new-dtags -L/home/soft/centOS/compilers/gcc/openmpi/4.1.4/lib -Wl,-rpath -Wl,/home/soft/centOS/compilers/gcc/openmpi/4.1.4/lib -Wl,–enable-new-dtags -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/openblas-0.3.20/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/openblas-0.3.20/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/fftw-3.3.10/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/fftw-3.3.10/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxc-5.2.3/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxc-5.2.3/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxsmm-1.17/lib’ -Wl,-rpath=‘/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/libxsmm-1.17/lib’ -L’/home/chemistry/phd/cyz208667/Softwares/new_cp2k/cp2k-2022.1/tools/toolchain/install/scalapack-2.1.0/lib’ LIBS=…

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Installation error of GMX+CP2K on WSL – User discussions

GROMACS version: 2023GROMACS modification: Yes/No Dear Gromacs community: I tried to install GROMACS 2023 in combination with CP2K.2023.1 on WSL.I successfully install cp2k.2023.1 and tried to install gromacs, then I got this error at the end: [100%] Building CXX object src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o [100%] Building CXX object src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o [100%] Built target gmx_objlib…

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Fixed atoms in geometry optimization

Dear CP2K  users, I would like to run a geometry optimization while keeping all atoms except hydrogen atoms fixed. I used the following sections in the input file with a list of around 750 atoms:  &MOTION   &CONSTRAINT     &FIXED_ATOMS       LIST 1 3 4 …      &END FIXED_ATOMS …

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Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation

I hope this email finds you well. I have a query regarding my CP2K AIMD simulation involving a water box with periodic boundary conditions (PBC) in the XY direction. Here is an excerpt from my input file:     &CELL      ABC 24.4797   24.4797  200.0      ALPHA_BETA_GAMMA…

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Problem with CP2K running AIMD

Dear cp2k users, I have met serious problem with cp2k running AIMD. I complied CP2K 2023.1 with gcc.9.3.0 and intelmpi. First, I ran the test1.inp file and found that after 20 electronic steps, the computation time suddenly increased for each step, and the time became increasingly longer, making it impossible to proceed. However,…

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Obtaining the Wannier Hamiltonian from CP2K

Dear CP2K users, In my research I usually use Wannier90 software to obtain the Wannier centers and Wannier Hamiltonian from a QuantumEspresso output, so I can calculate the magnetic exchange couplings using TB2J . Now I am starting to use CP2K and I am trying to underestand the section &LOCALIZE….

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Spin specific constraints in CDFT

Hi, I am trying to carry out Constrained DFT calculations for a chloride radical transfer reaction between tert-butyl hypochlorite and a benzyl radical. Part of this requires mixed CDFT calculations, with spin specific constraints. Here, I’m using  TYPE_OF_CONSTRAINT BECKE (in the &CDFT section) CONSTRAINT_TYPE ALPHA (in the &ATOM_GROUP section) However,…

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Unexpected 0D wavelet errors at large vacuum

Hi it works for me (CP2K Trunk version) Precond_solver : DEFAULT stepsize : 0.08000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ———————————– OT ————————————— Step Update method Time Convergence Total energy Change —————————————————————————— 1 OT DIIS 0.80E-01 7.1 0.10459074 -83.0126092838 -8.30E+01 2 OT DIIS 0.80E-01 7.0 0.07934045 -85.4719301173 -2.46E+00 3 OT DIIS 0.80E-01 7.3 0.04237559…

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Most Demanding Players, Share, Industry Analysis of Future Demand, Opportunities, Forecast and Growth Rate To 2030

PRESS RELEASE Published July 3, 2023 Complete Research on Bioinformatics Software Market: Help to gain Knowledge of industry peers, upcoming trend, scope and factor affecting growth and development by 2023-2030. The updated Global “Bioinformatics Software Market” report for 2023 delves into several crucial components that are essential to the market…

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CP2K_INPUT / FORCE_EVAL / QMMM / CELL

List of valid keywords: CUBIC Cubic (a = b = c, α = β = γ = 90°) HEXAGONAL Hexagonal (a = b ≠ c, α = β = 90°, γ = 60°) MONOCLINIC Monoclinic (a ≠ b ≠ c ≠ a, α = γ = 90°, β ≠ 90°)…

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Convergence problem with cobalt oxide Cu3O4

Dear CP2K users, I am currently working with a series of transition metal oxides and CP2K is working fine but when I try to converge a calculation on the mixed valence Cu oxide (Cu3O4) my calculations are not converging. I have read that this oxide is a tricky system for…

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Help on adding limit potential to do AIMD simulation in CP2K

Dear all, I wanted to do a simulation of water molecules inducing catalyst surface remodeling, so I wanted to implement the addition of a limiting potential to bring water molecules close to the catalyst surface, leading to catalyst surface remodeling. This was done by referring to the SI section of…

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A problem while using the M06/TZVP

Hello,   I need to use cp2k to calculate the cell parameters and vibration frequency of UIO-66 with m06 functional and tzvp basis set.(I want to use the def2-tzvp but there is no such basis sets for zirconium in cp2k)   However, I found that the calculated results of m06/tzvp…

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Errors of parallel compilation of cp2k 2023.1

Hi all, I tried to run the toolchain script by the following options: ./install_cp2k_toolchain.sh –with-intel=system –with-gcc=no –mpi-mode=openmpi –math-mode=mkl –with-cmake=system –with-libint=no –with-libxsmm=no –with-elpa=no –with-pexsi=no –with-quip=no –with-plumed=no –with-spglib=install –with-cosma=no –with-libvori=no –with-gsl=no –with-spfft=no –with-hdf5=no –with-spla=no –with-mkl=system  –with-fftw=install –with-libxc=install –with-sirius=install After revision of the generated local.psmp file, I tried to make the code by the…

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Compilation error of cp2k 2023.1 on ubuntu

Hi, all Following the instruction online step by step, I tried to install cp2k 2023.1 on ubuntu 22.04.2 Errors appeared as I try to make it Need your help to remove this error jibiaoli@ubuntua:~/codes/cp2k/arch$ make -j 104 ARCH=local VERSION=ssmp … … /home/jibiaoli/intel/oneapi/compiler/latest/linux/bin/intel64/ifort -c -fopenmp -fp-model precise -g -nofor-main -qopenmp-simd -traceback…

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The example input of water molecule ran into error

I tried to run the example file online by the command “cp2k.ssmp -o water.out water.inp &’, but the calculations aborted with the following error. Need your help. … …   SCF WAVEFUNCTION OPTIMIZATION   Step     Update method      Time    Convergence         Total energy    Change  …

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GW100 calculation and S2p line fine structure

Dear CP2K users   I would like to calculate core electron binding energy using GW100 method in CP2K. www.cp2k.org/howto:gw   I started with a simple test, using a sulfate ion, SO42-, in vacuum to calculate the S2p lines. I first optimized the structure of SO42- in vacuum at PBE level,…

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Compilation errors of CP2K on ubuntu

Hi, all I am new to LINUX and CP2K. I tried to get the code using the command: then I tried to make the code using the command: make -j 8 ARCH=Linux-intel-x86_64 VERSION=psmp but errors appeared: Resolving dependencies … /usr/bin/env python3 /home/jibiaoli/codes/cp2k/exts/dbcsr/tools/build_utils/fypp/bin/fypp -n /home/jibiaoli/codes/cp2k/exts/dbcsr/src/base/dbcsr_machine.F dbcsr_machine.F90mpiifort -c -O2 -fopenmp -fp-model precise…

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k-points vs. supercell approach

Dear CP2K community, I’m quite new to CP2K and I am trying to build my input files step-by-step to eventually do calculations on modified surfaces. Currently I’m still doing single point calculations on my bulk structure (anatase TiO2) to optimize the calculation parameters. I have already converged the values of…

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GEO_OPT towards higher energy with DFU+U method

Dear CP2K developers and users, I am running a geometry optimization job with DFT+U method. I cannot get convergence with MULLIKEN method but LOWDIN. The force and step criterion is reached, however, the system goes to higher energy during optimization. The output file is attched. I guess the force calculation…

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Regarding using Plumed as an external engine for OPES Metadynamics in Cp2k

I am attempting to run OPES Metadynamics in CP2K, using PLUMED as an external driver. I am encountering two problems with my setup: =================================== plumed_inupt_file UNITS LENGTH=A ENERGY=kcal/mol TIME=fscv1: DISTANCE ATOMS=4,13cv2: DISTANCE ATOMS=1,16opes: OPES_METAD_EXPLORE ARG=cv1,cv2 PACE=20 BARRIER=50 TEMP=300uwall: UPPER_WALLS ARG=cv1,cv2 AT=3.0,3.0 KAPPA=40,40PRINT STRIDE=20 FILE=COLVAR ARG=* ======================================= When I omit the…

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molecular polarizability calculated via cp2k is different from psi4 and gaussian09

I am trying to calculate molecular polarizability of a single CH4 molecular via cp2k software using the B3LYP functional and the d-aug-cc-pVDZ basis set. The strategy is as follows. By changing the polarization direction of the electric field, the corresponding molecular dipole moment is obtained, and then the molecular polarizability…

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Incorrect optimized geometry using CELL_OPT

Dear CP2K users, I am kind of new using cp2k but I have been using the software fo a couple of months. I am trying to optimize both geometry and cell parameters of different semiconductor material but the obtained geometries are distorted compared with experimental data or relaxed geometries obtained…

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GEMC module does not keep stable liquid and vapor phases for water

Dear CP2K Developers, I am looking into using the Gibbs Ensemble Monte Carlo (GEMC) methos in CP2K to compute the liquid-vapor phase diagram using a fully DFT-based method. However, I have problems stabilizing liquid and vapor phases when doing simulations fully ab intio, as described below. By taking input files…

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Bioinformatics Software Market Will Touch New Level in Upcoming Year

PRESS RELEASE Published May 29, 2023 Bioinformatics Software Market Analysis 2023 | by Product Type ( Knowledge Management Tools, Bioinformatics Platforms, Bioinformatics Services ), Application Type ( Medical bioinformatics, Animal bioinformatics, Agricultural bioinformatics, Scholars and microbial genomes, ), CAGR, Major Key Players are covered in this report by 360 Market…

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