Tag: GROMACS

Gromacs: nbnxn_sci Struct Reference

#include <gromacs/nbnxm/pairlist.h> Description Grouped pair-list i-unit. Public Member Functions int  numJClusterGroups () const   Returns the number of j-cluster groups in this entry.   Public Attributes int  sci   i-super-cluster   int  shift   Shift vector index plus possible flags.   int  cjPackedBegin   Start index into cjPacked.   int …

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High-Performance Computing Software Market Future Scope

Marketreports.info has unveiled the addition of a new study titled Global High-Performance Computing Software Market, which incorporates regional and global price information and is expected to earn a profitable worth between 2022 and 2030. The research defines the market, designates it, describes its operations, interactions, and global High-Performance Computing Software…

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Thermostat and barostat in equilibration phase in a membrane-protein system – User discussions

Davidb November 9, 2022, 10:50am #1 GROMACS version: gromacs-2022GROMACS modification: Yes/No Hi, I am using CHARMM-GUI generated system of a transporter protein in a membrane bilayer. In the equilibration phase, the recommended workflow from CHARMM-GUI is to use Berendsen for both temperature and pressure (semi-isotropic). However, gromacs highly discourage it,…

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High-Performance Computing Software Market Forecast 2022 Analysis of The Key Players, Growth Status, Business Strategies and Scope with Outlook 2030

Read Time:4 Minute, 46 Second New York (US) – Key Companies Covered in the High-Performance Computing Software Market Research are Altair Engineering, Ansys, Dassault Systemes, ESI, Gaussian, Gromacs, Livermore Software, Siemens and other key market players. The global High-Performance Computing Software Market is expected to reach US$ Million by 2027, with a CAGR of $$%…

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Is it possible to output the topology file without include – User discussions

zhiyiwu October 26, 2022, 2:31pm #1 I’m interested in parsing the Gromacs topology file for my analysis script. However, the include fields are making my life harder. I wonder if there is a gmx command that takes in a gmx topology with those include fields and then output a topology…

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Molecular Dynamics Software Market Size, Historical Growth, Analysis, Opportunities and Forecast To 2026

The Molecular Dynamics Software market research focuses on the major economic changes that are projected to occur between 2022 and 2028. The primary focus of analysis is on factors that may influence how the firm sector progresses, such as growth boosters, inhibitors, and other potential opportunities. According…

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Protein-protein Simulation RMSD, energy scoring, etc – User discussions

mike October 14, 2022, 1:29am #1 GROMACS version: 2022.3GROMACS modification: Yes/NoHere post your question I am performing a protein-protein MD simulation, however I am running into an issue such as listed below, where it says “Protein” I can’t distinguish between the two proteins being docked. How would I create an…

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Ubuntu Manpage: csg_fmatch – Part of the VOTCA package

Provided by: votca-csg_2021.2-1_amd64 NAME csg_fmatch – Part of the VOTCA package SYNOPSIS csg_fmatch [OPTION] [OPTIONPARAMETERS] DESCRIPTION Perform force matching (also called multiscale coarse-graining) Please visit the program site at __http://www.votca.org__. OPTIONS Allowed options: -h [ –help ] display this help and exit –verbose be loud and noisy –verbose1 be very…

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High-Performance Computing Software Market to Witness Huge Growth by 2029 -Altair Engineering, Ansys, Dassault Systemes, ESI, Gaussian, Gromacs, Livermore Software, Siemens

New Jersey, United States,- Mr Accuracy Reports , High-Performance Computing Software market report contains detailed information on factors influencing demand, growth, opportunities, challenges, and restraints. It provides detailed information about the structure and prospects for global and regional industries. In addition, the report includes data on research & development, new product launches,…

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The determination of the effect(s) of solute carrier family 22-member 2 (SLC22A2) haplotype variants on drug binding via molecular dynamic simulation systems

International Diabetes Federation (IDF). Diabetes Atlas 8th Edition 2017. www.idf.org/our-network/regions-members/africa/welcome.html. Accessed 15 July 2018 (2018). Singh, S., Usman, K. & Banerjee, M. Pharmacogenetic studies update in type 2 diabetes mellitus. World J. Diabetes. 7, 302. doi.org/10.4239/wjd.v7.i15.302 (2016). Article  PubMed  PubMed Central  Google Scholar  Inzucchi, S. E. et al. Management of…

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Gromacs: gmx::anonymous_namespace{electricfield.cpp}::ElectricField Class Reference

Describe time dependent electric field. Class that implements a force to be evaluated in mdrun. The electric field can be pulsed and oscillating, simply oscillating, or static, in each of X,Y,Z directions. Initializes a transform from mdp values to sectioned options. The transform is specified from a flat KeyValueTreeObject that…

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How To Install Eneconv On Debian, Ubuntu, Kali, Fedora, Raspbian And MacOS?

eneconv Molecular dynamics simulator, with building and analysis tools Maintainer: Debichem Team Section: science Install eneconv Debian apt-get install gromacs Click to copy Ubuntu apt-get install gromacs Click to copy Kali Linux apt-get install gromacs Click to copy Fedora dnf install gromacs Click to copy Raspbian apt-get install gromacs Click…

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[gmx-users] box type

Post by Sana Saeedhi gmx userscan we use truncated octahedron as -bt (box type) in gromacs. The user manual knows the answer. -Justin—================================================== Justin A. Lemkul, Ph.D.Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical SciencesSchool of PharmacyHealth Sciences Facility II, Room 629University of Maryland, Baltimore20 Penn St.Baltimore, MD 21201…

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Gromacs 2021 + cp2k – User discussions

GROMACS version: 2021.2GROMACS modification: No Hello GROMACS users and developers. I have a demand to compile GROMACS 2021.2 with CP2K 9.1. Is this combination supported? If so, how to do it? I noticed that the cmake variables DGMX_CP2K, DCP2K_DIR and DCP2K_LINKER_FLAGS are available only in the 2022 version. And from…

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Make check failure – User discussions

GROMACS version: 2022.02GROMACS modification: No failed in “make” using gcc/g++ ver. 11after downgrading to ver. 10in make check:99% tests passed, 1 tests failed out of 88 Label Time Summary:GTest = 300.14 secproc (81 tests)IntegrationTest = 137.11 secproc (25 tests)MpiTest = 191.06 secproc (19 tests)QuickGpuTest = 34.88 secproc (17 tests)SlowTest =…

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Scientific Software Development Infrastructure – LiU PDF Documents Library

Scientific SoftwareDevelopment InfrastructureRossen ApostolovKTH/[email protected] A use case:GROMACS GROMACS Project started 1995 in Groningen, most of the core developersare now in Sweden Highly tuned code for molecular dynamics, minimization, normalmode analysis; post-processing tools ( 100) Open source & Free software: L-GPL 3000-5000 users world wide, through [email protected] 300kactive CPUs, Apr. 2012…

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A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis

Pérez-Serra, A. et al. Genetic basis of dilated cardiomyopathy. Int. J. Cardiol. 224, 461–472 (2016). PubMed  Article  Google Scholar  Petropoulou, E. et al. Digenic inheritance of mutations in the cardiac troponin (TNNT2) and cardiac beta myosin heavy chain (MYH7) as the cause of severe dilated cardiomyopathy. Eur. J. Med. Genet….

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Is it possible to use umbrella sampling to simulate the complex membrane model? – User discussions

GROMACS version: 2021.2 HiI need to make some natural pore in the membrane model that contains the different types of lipids (with an asymmetric lipid distribution between the bilayer leaflets) for studying change in these pores under special conditions. I have never done umbrella sampling and I don’t know about…

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GROMACS Installation Problem in The Grid Computer – User discussions

GROMACS version: 2021.2GROMACS modification: No Hello all, I am new to GROMACS. I wanted to install it on a grid computer servers supported by the government and I’ve done step by step instructions in the following link (The language of the instructions is in Turkish but you may find the…

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[gmx-users] dssp

Hi,I have a problem with dssp programme.I have the programme in /home/m/DSSP. When I writeexport DSSP=/usr/local/binand then I check /usr/local/bin I couldn’t see dssp.How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written.Could you write export DSSP=/path/to/dssp command according to me….

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Molecular Dynamics Software market share from APAC, Europe, America application to rise at XX% CAGR through 2028

added a new report on Molecular Dynamics Software market with respect to the pivotal drivers influencing the revenue graph of this business sphere. The current trends of Molecular Dynamics Software market in conjunction with the geographical landscape, demand spectrum, remuneration scale, and growth graph of this vertical…

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Running Protein simulation with multiple ligands – User discussions

GROMACS version: 2018 Hello everyone,I am new to GROMACS and trying to run a protein simulation with chromophores FAD and DLZ and DNA as ligands using Amber ff99sb force field. While running the simulation how should I generate the index files for the chromophores? Should I generate three different index…

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Error While Adding Ions.Please Help. Urgent – User discussions

GROMACS version:GROMACS modification: Yes/NoHere post your question ERROR 1 [file topol.top, line 14284]:No default Proper Dih. types ERROR 2 [file topol.top, line 14304]:No default Proper Dih. types I am facing two errors. It shows like this. PLEASE HELP. 376 377 378 379 1 gd_12376 381 383 385 1 gd_4381 383…

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Error when adding new residue to hdb (CHARMM36) – User discussions

dom June 26, 2022, 2:05am #1 GROMACS version:2022.2GROMACS modification: No I am adding a new protein residue to the CHARMM36 forcefield (July 2021). As per the instructions in the GROMACS manual (“Adding a Residue to a Force Field”), I modified residuetypes.dat, aminoacids.rtp, and aminoacids.hdb with the new residue entry. It…

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ERROR No such moleculetype NA – User discussions

GROMACS version:GROMACS modification: Yes/No I got this errorwhen I run the line: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 10in the topol.top there is 3 NA atoms 🙂 GROMACS – gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C….

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Molecular Dynamics Simulation Software Market by 2029

New Jersey (United States) – A2Z Market Research published new research on Global Molecular Dynamics Simulation Software covering the micro-level of analysis by competitors and key business segments (2022-2029). The Global Molecular Dynamics Simulation Software explores a comprehensive study on various segments like opportunities, size, development, innovation, sales, and overall…

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Creating nacl in water system – User discussions

GROMACS version: 2018.6GROMACS modification: No I am very new to using gromacs, so I would appreciate any input.I am trying to set up a system of NaCl (JC) in water(spce) . I was able to run the tutorial simulation of lysozome in water. But in this the topology file was…

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Porting GROMACS Across Heterogeneous Architectures

Porting GROMACS Across Heterogeneous Architectures In this second episode about GROMACS, one of the world’s most widely used open source molecular dynamics (MD) applications, we explore the quest to simplify portable, performant programming with Erik Lindahl, Biophysics Professor at Stockholm University & KTH Royal Institute of Technology, and Roland Schulz,…

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Regarding the use of -table and -tablep – User discussions

GROMACS version: 2018.3GROMACS modification: No Hi, I am trying to simulate a polymer-water system where the polymer beads interact by Weeks-Chandler-Andersen potential and all the other non-bonded interactions are LJ type. I have two tabulated potential files: (i) table.xvg (for LJ) and (ii) table_P_P.xvg (for WCA). In the .mdp file…

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How to calculate total interaction energy between protein and polyethylene surface – User discussions

Teabo May 9, 2022, 4:03am #1 GROMACS version: Gromacs 2018GROMACS modification: NoHere post your questionDear all,I have a system including one protein and one polyethylene layer. I wonder how to calculate the interaction energy between the protein and the polyethylene layer, should I use gmx enemat? Or could anyone suggest…

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[gmx-users] Gromacs 5.1 – trouble with insert-molecules

I think I answered this a week ago. Post by Dan GilHi,I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had “genbox,”which I was able to use without a problem.With gromacs 5.1, I am using insert-molecules to generate my initialconfiguration containing water, ethanol, and a lennard-jones particle whichI…

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Accepted gromacs 2022.1-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 22 Apr 2022 18:22:17 -0700 Source: gromacs Architecture: source Version: 2022.1-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Closes: 1009383 Changes: gromacs (2022.1-1) experimental; urgency=medium . * New upstream release. * Restore mdrun-test-timeout.patch, to handle…

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SwissDock and Autodock Vina results comparison : comp_chem

Hi! I’m a chemistry undergrad. For my research, I performed docking using Autodock Vina. For further validation, I tried docking using SwissDock too. But now, the two programs give different results. They predict different ligands to give the most favorable binding. I read that Autodock is more reliable. So, should…

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Molecular Dynamics Software Market Growing Popularity & Emerging Trends

The latest independent research document on Molecular Dynamics Software examine investment in Market. It describes how companies deploying these technologies across various industry verticals aim to explore its potential to become a major business disrupter. The Molecular Dynamics Software study eludes very useful reviews & strategic assessment including the generic market…

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Density profile along the interface normal – User discussions

Dear all,I’d like to observe how density varies within the box, therefore could someone please explain how to find density within each of the slices of a simulation box formed by slicing the simulation cell into 1 angstrom-partitions along the z axis? Sasha April 15, 2022, 9:48am #2 gmx density:…

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Bioinformatics Software Market Outlook: Post Covid-19 Scenario by 2029

California (United States) – The Bioinformatics Software Market Research Report is a professional asset that provides dynamic and statistical insights into regional and global markets. It includes a comprehensive study of the current scenario to safeguard the trends and prospects of the market. Bioinformatics Software Research reports also track future…

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How to combine OPLS-AA with Berger lipids? Links in tutorial dead – User discussions

Isolde April 13, 2022, 2:15am #1 GROMACS version: 2022GROMACS modification: No Greetings! I would like to simulate a small molecule (described by OPLS-AA) interacting with a POPC bilayer (Berger lipids). However, the links in the GROMACS membrane tutorial (see below) that should lead to instructions on how exactly to combine…

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No default type errors -NH2 and COO- amino acid termini patches for pH 10 simulations – User discussions

GROMACS version:2022GROMACS modification: NoMuch thanks for any help and guidance on these errors – I am studying mixtures of amino acids at pH 10; at this pH the N-term is neutral NH2 and the C-term is negative COO-. I am using the charmm27 force field to parametrize and patch each…

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GROMACS+CP2K Single vs Double Precision – User discussions

cbl123 April 4, 2022, 8:38pm #1 GROMACS version: 2022GROMACS modification: Yes/No (CP2K) Hello dear users and devs, I would like to know if there’s major implications in the accuracy of my calculations if I use single precision instead of the recommended double precision for QM/MM calculations with Gromacs 2022+CP2K. Thanks…

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Loading environment modules on a cluster from my python script

I recently ran into this. A simple way around this would be to include the dependencies before the command you want, and separate them with a semi-colon cmd = ‘module load intel/2016.4; “gromacs command”‘ p = sub.Popen(cmd, shell=True, stderr = sub.STDOUT, stdout = sub.PIPE).communicate()[0] where “gromacs command” represents however you…

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Double precision on gro file using editconf – User discussions

GROMACS version:2022.1GROMACS modification: NoIs there a way to keep the position coordinate in DP? The gro file seems to revert back to SP when it get converted from pdb to gro by editconf. I can rewrite them into DP but I do not know how to keep DP when the…

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[gmx-users] template.c is needed for Gromacs 5.0

Hi, Unfortunately, no. The whole project has been moving to C++ for some years.Writing the template in object-oriented C would look (and work) even worse😉 If you’ve got some specific feedback about what’s hard to understand,we’re happy to consider improvements! 🙂 Mark Post by BertHi all,I used to write my…

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Understanding the implementation of the virtual sites in gromacs – User discussions

GROMACS version: 2020.5GROMACS modification: NoI am building a CG model using virtual particles. I defined the virtual particle on the basis of the position of the neighboring particles and distributed the mass of that particular particle which I want to make virtual to the corresponding neighboring particles. My understanding is…

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Oops! That page doesn’t exist or is private.

Sign Up Log In Log In Popular “make check” Test 1 fails for Gromacs 2022User discussions DNA ending effectUser discussions GROMACS 2022 official releaseAnnouncements Basic questions about constant pH simulationUser discussions File input/output error: tprout.tprUser discussions 2022 Regression Test TimeoutsUser discussions Why is mpi thinking gromacs args are for mpi?User…

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Gromacs performance on GPU – User discussions

GROMACS version: 2022GROMACS modification: Yes/No Hi! I am checking the performance of my fresh Gromacs installation on a new PC. I have the newest Gromcas compiled (Linux Mint) using the basic scheme from the manual with added support for Nvidia GPU (CUDA, 11.60). CPU is AMD Ryzen 9 5950X (16…

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Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

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Gromacs: src/gromacs/selection/selmethod.cpp File Reference

#include “gmxpre.h” #include “selmethod.h” #include <cctype> #include <cstdarg> #include “gromacs/utility/arraysize.h” #include “gromacs/utility/cstringutil.h” #include “gromacs/utility/exceptions.h” #include “gromacs/utility/stringutil.h” #include “selmethod-impl.h” #include “symrec.h” This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements functions in selmethod.h. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com static void  report_error (FILE *fp, const char…

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Fatal error: Invalid line in complex.gro for atom 5185: 9.36900 9.36900 16.01200 – User discussions

GROMACS version: 2020.1GROMACS modification: NoHello everyone, i get error message like this when define unit cell gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.5 Fatal error:Invalid line in complex.gro for atom 5185: 9.36900 9.36900 16.01200Previously I have also done simulations with other ligands and it worked. anyone can…

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Nvt.tpr -I couldn’t manage my nvt.tpr – User discussions

GROMACS version:2022-cp2k interface I couldn’t manage my nvt.tpr I tried to fix problem but I couldn’t. gmx_cp2k grompp -f nvt.mdp -c confout.gro -r confout.gro -p topol.top -n index.ndx -o nvt.tpr nvt.mdb file :; md-nvt.mdp – used as input into grompp to generate nma-nvt.tprintegrator = md ; MD using leap-frog integratordt…

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Gmxapi gromacs 2022 error – User discussions

. /path/to/gromacs/bin/GMXRC You used the actual installation path here, right? ╰─> [124 lines of output] We can’t help without the full output. Please copy the raw text from the terminal window. Note that you can format the terminal output in the forum post either by using the </> button or…

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Issue with gmx extract-cluster – User discussions

GROMACS version: 2020.1GROMACS modification: No Hello Gromacs users, I need to extract a set of frames from my trajectory and I have the index of these frames (the frame number, not time). With gromacs version before 2020, I used to create an index file and then extract the conformations with…

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Gromacs: gmx::DomDecHelper Class Reference

Infrastructure element responsible for domain decomposition. This encapsulates the function call to domain decomposition, which is important for performance but outside of the current scope of the modular simulator project. This relies on legacy data structures for the state and the topology. This element does not implement the ISimulatorElement interface,…

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Change of protein-protein-interaction free energy upon ligand binding (procedure and controls) – User discussions

GROMACS version: 2021.1GROMACS modification: No Dear Gromacs and simulation community, in the course of my master’s thesis, I want to determine the protein-protein-binding free energy between two GTPases using PMF calculations via umbrella sampling. Especially I am interested in the contribution of the bound nucleotides (one per protein) which are…

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trollchu | coder – Coder Social

Qingzhao’s Projects AI-learns-to-play-the-dino-game AsFem A Simple Finite Element Method program (AsFem) aten Molecular / atomic coordinate editor atomman Atomistic Manipulation Toolkit awesome-python-chemistry A curated list of Python packages related to chemistry awesome-python-MD cantera Chemical kinetics, thermodynamics, and transport tool suite CFDPython A sequence of Jupyter notebooks featuring the “12 Steps…

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GROMACS – SBGrid Consortium – Supported Software

Usage Notes SBGrid Usage Info GROMACS is GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : sbgrid.org/wiki/gpu CUDA builds of GROMACS are designated by a ‘_cu’ suffix in the version of the application. For example, 2020.2_cu9.2.88 is linked against…

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Regarding the use of WCA and Attractive inteactions simultaneously – User discussions

GROMACS version: 2018.3GROMACS modification: No Hello Gromacs users, I am trying to simulate a system where some of the particles (type-A) obey WCA potential and some (type-B) obey an attractive potential (user defined). And there A-B interaction follows another (user defined) poential form. I have used tabulated potentials but not…

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LJ parameters – User discussions

GROMACS version: 2021.3GROMACS modification: NoHere post your question I have a very basic question on parameterization of non-bonded parameters (LJ) of atoms. The target system is a cluster/aggregate of metal atoms. From experimental data, I can get the atomic radius and vdw radius of the atoms. However, looking at the…

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Issue with segmentation fault – User discussions

GROMACS version: 2021.2, 2019.6GROMACS modification: YesHere post your question I am facing a segmentation fault issue with GROMACS patched with plumed and I was wondering if you could help me. I am trying to run a replica averaged MD simulation by calculating the backbone chemical shifts for a protein (using…

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molecular dynamics – How to generate a .tpr file from a .pdb or .xyz file in gromacs

For generating a tpr file, you need a topology file (.top), a coordinate file (.gro/.pdb) and a input parameter file (.mdp). Assuming, you are working with amber forcefield (a99ffSBdisp), Here’s how I do it. gmx pdb2gmx -ff a99SBdisp -f yourpdbfile.pdb -o water_1.gro -ignh -p topol.top gmx grompp -f water.mdp -c…

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How to generate a free energy Ramachandran plot from a GROMACS MD trajectory if protein has more than 2 residues? : comp_chem

I ran some REMD calculations with GROMACS and wish to create a plot which depicts the free energies of the different regions on the Ramachandran plot of my protein at a specific temperature, similar to figure 2 in the following paper below. Article Antifreeze Glycoproteins Bind Reversibly to Ice via…

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Gromacs: gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf Class Reference

Public Member Functions virtual void  initOptions (IOptionsContainer *options, TrajectoryAnalysisSettings *settings)   Initializes options understood by the module. More…   virtual void  optionsFinished (TrajectoryAnalysisSettings *settings)   Called after all option values have been set. More…   virtual void  initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top)   Initializes the analysis. More…  …

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[gmx-users] why not coordinates from cpt file

Post by gromacs queryHi allI have very simple query. While continuing simulations why we need to use*.gro (-c) with grompp as *.cpt (-t) has all the information (as checkedwith gmxcheck)?cpt file should suffice all the purposes. I tried using grompp providing -t*.cpt file but without -c *.gro file, it does…

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[gmx-users] Adaptive Biasing Force method

Post by k***@mech.sharif.irDear GROMACS usersIs there any way� to employ the adaptive biasing force (ABF) methodwith GROMACS ?! If so,� could you please introduce me a tutorial orarticle about it ? I really appreciate it. Available features are described in the manual. Tutorials are found via Google. -Justin—================================================== Justin A….

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[gmx-users] sudden jumps in RMSD etc.

Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, Istill find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then…

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Gromacs: src/gromacs/nbnxm/kernels_reference Directory Reference

Directory dependency graph for kernels_reference: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   kernel_gpu_ref.cpp   file   kernel_gpu_ref.h   Declares GPU reference kernel.   file   kernel_ref.cpp   file   kernel_ref.h   Declares CPU reference kernels.   file   kernel_ref_includes.h…

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Accepted gromacs 2022~rc1-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 29 Jan 2022 10:08:31 -0800 Source: gromacs Architecture: source Version: 2022~rc1-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2022~rc1-1) experimental; urgency=medium . * New upstream release candidate. * Drop hppa-disable-ewaldunittest.patch. * Set build…

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[gmx-users] Regarding combination rules in gromos53a6 ff

Dear GROMACS users,I want to use the geometric mean of both sigma (sigma i sigmaj)andepsilon(epsilon i epsilon j) as a combination rule in my simulation.According to the combination rules in the manual, the combination 3incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)Cj(6) and Ci(12)Cj(12) terms.So can I…

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[gmx-users] Is such hardware suitable for gromacs

Your mail looks like spam at first glance. Surely. They can be used to run Gromacs. In fact, Gromacs welcomes bothIntel and AMD’ modern CPU with SIMD capability. To build a small cluster, you also need some networking devices: a GBether switch and some good cables. Rest is software installation…

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[gmx-users] Why gyration radius keep dropping?

Post by ZHANG ChengDear Gromacs,I am running MD at 500 K for my protein.I used this to analyse the gyration radiusecho 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvgI thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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Building Modified DNA topology – User discussions

GROMACS version: 2021.4GROMACS modification: Yes/NoHere post your question I am having trouble generating topology for a type of modified DNA, but I’m not sure how to do it.In fact, there is a 35-nucleotide sequence of ssDNA. Using the Discovery Studio program, I converted the Thymidine Oxygen 4 atom to Sulfur…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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[gmx-users] grompp -check14

Post by Dongsheng ZhangDear all,Has anyone used -check14 for grompp? When I tried it just now, I gotsegmentation fault. grompp works fine without the option -check14 (orgrompp -f md01.mdp -c ala5 -p ala5 -check14 -o fullBack Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency…calling /lib/cpp…processing topology…Generated…

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[gmx-users] Scaling in gromacs

Dear GMX users In order to benchmark my simulation system I would like to know in gromacswhich code scales linearly till 10K cores? ThanksBest RegardsPraveen—Thanks & RegardsDr. Praveen Kumar Sappidi,DST-National Postdoctoral FellowComputational Nanoscience LabChemical Engineering Department,IIT Kanpur —Gromacs Users mailing list * Please search the archive at www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!…

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[gmx-users] The grompp problem!! (Urgently)

I am doing the Drug-enzyme tutorial.I also generated the drg.itp, drg.gro files using PRODRG server.However, when I use the grompp command before the energy minimizationI face some error A fatal error was shown: atom types CR61 not found The atom type CR61 is presented in the drg.itp file that I…

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Comprehensive, hands-on tutorial for DNA-ligand MDS – User discussions

GROMACS version: 2021.4-HomebrewGROMACS modification: No Hello, guys. I am very new to molecular dynamics and I come from biomedical background. Recently, my boss asked me to gather additional data about interaction of a small molecule and an aberrant double-stranded DNA structure. I originally did docking experiments in Vina, and he…

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Bio/pharma vs. materials – can anyone speak of specializing in either of these? : comp_chem

It seems like most comp chemists lie on the spectrum in terms of their research application, which spreads from biochemical (proteins, drug design, biomolecular simulations, etc.) to inorganic materials (semiconductors, minerals/crystals, battery/electrolytes, alloys, metals, etc.). I think it’s a notable spectrum because these fields have entirely different software suites dedicated…

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runing a command multiple times in different nodes in SLURM

I want to run three instances of GROMACS mdrun on three different nodes. I have three temperatures 200,220 and 240 K and I want to run 200 K simulation on node 1, 220 K simulation on node 2 and 240 K simulation on node 3. I need to do all…

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[gmx-users] abnormal stop of job

In tis case it must have been your sysadmin or your queueing system. Check the other answers in this thread. Post by Samrat PalHi Elton,But I have neither killed the job nor I pressed Ctrl-C in the foreground.The job was practically running background.ThanksAtanu________________________________From: Elton Carvalho To: Discussion list for GROMACS…

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[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field.While running energy minimization I did get the error“No default Ryckaert-Bell. types”. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO)has No default Ryckaert-Bell. types. but on checking ffbonded.itp I foundthat this dihedral is…

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How to simulate peptide solubility using molecular dynamics (GROMACS)?

SCIENCE By mattermodeling.stackexchange.com | 11 hours ago I’m not sure why you would use radius for gyration as a measure of solubility. Radius of gyration roughly measures how “unfolded” (or more accurately, how “stretched out”) a polymer is. Although this may correspond to a higher solvent accessible surface area (which…

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molecular dynamics – How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

Which is more appropriate for the binding energy? Neither. Obi-Wan voice: “These are not the energies you’re looking for.” If I understand your goal, you’re trying to compare two ligands and determine which is better at binding to a given protein (and, ideally, quantify “how much better” one is compared…

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molecular dynamics – How to manage disk space for Gromacs XTC (trajectory) file output

Is there an option in gmx mdrun to specify where to write the .xtc file? For example I want to specify specific directory path with large disk space. When you use the -deffnm md argument to gmx mdrun, it is assumed that all of the files will have the base…

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[100% Off UDEMY Coupon] – Molecular Dynamic Simulation on Gromacs Software –

Using this 100% off UDEMY Free Coupon Code, you can able to enroll the course: Molecular Dynamic Simulation on Gromacs Software for Free on Udemy.This is a UDEMY Free Promo Code this is totally Free for a Limited Time so enroll soon as possible Molecular Dynamics Simulations ,Gromacs Software ,MD…

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Gromacs: src/gromacs/gmxpreprocess Directory Reference

Directory dependency graph for gmxpreprocess: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Directories directory   tests   Files file   add_par.c   file   add_par.h   file   calch.c   file   calch.h   file   convparm.c   file   convparm.h  …

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Gromacs: gmx::GpuBonded::Impl Class Reference

#include <gromacs/listed-forces/gpubonded-impl.h>   Impl (const gmx_ffparams_t &ffparams, void *streamPtr)   Constructor.     ~Impl ()   Destructor, non-default needed for freeing device-side buffers.   void  updateInteractionListsAndDeviceBuffers (ArrayRef< const int > nbnxnAtomOrder, const t_idef &idef, void *xqDevice, void *forceDevice, void *fshiftDevice)   Update lists of interactions from idef suitable for the…

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Gromacs: gmx::LastStepSignaller Class Reference

#include <gromacs/modularsimulator/signallers.h> Inheritance diagram for gmx::LastStepSignaller: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Collaboration diagram for gmx::LastStepSignaller: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Description Element signalling the last step. This element…

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Accepted gromacs 2022~beta2-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Tue, 07 Dec 2021 19:29:05 -0800 Source: gromacs Architecture: source Version: 2022~beta2-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Changes: gromacs (2022~beta2-1) experimental; urgency=medium . * New upstream beta release. – gmx_x11.patch: Drop, applied upstream. -…

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Dual AMD EPYC 7773X Flagship Milan-X CPUs Benchmarked, Over 1.5 GB of Total CPU Cache On A Single Server Platform

New benchmarks of AMD’s upcoming Milan-X flagship, the EPYC 7773X CPU, have been submitted to the OpenBenchmarking software suite. AMD EPYC 7773X Milan-X CPUs With Up To 1.6 GB of Total CPU Cache Benchmarked In Dual Socket Server Platform The benchmarks were spotted within the OpenBenchmarking database and consist of…

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Accepted gromacs 2022~beta1-1 (source all amd64) into experimental, experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 26 Nov 2021 16:24:15 -0800 Source: gromacs Binary: gromacs gromacs-data gromacs-dbgsym libgromacs-dev libgromacs7 libgromacs7-dbgsym libnblib-dev libnblib0 libnblib0-dbgsym Architecture: source all amd64 Version: 2022~beta1-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Description: gromacs – Molecular dynamics…

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7643-gromacs-tyan-s8252 Benchmarks – OpenBenchmarking.org

2 x AMD EPYC 7643 48-Core testing with a TYAN S8252GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2112014-HOWE-7643GRO17 2 x AMD EPYC 7643 48-Core…

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7713-tyan-b8251-2u4g-gromacs Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a TYAN S8251GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111305-HOWE-7713TYA26 2 x AMD EPYC 7713 64-Core…

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Gromacs: src/gromacs/imd/imdsocket.h File Reference

#include “config.h”#include <netinet/in.h>#include <sys/socket.h> This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements the parts of the vmdsock.h interface needed for IMD communication. Author Martin Hoefling, Carsten Kutzner…

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7773X-gromacs Performance – OpenBenchmarking.org

2 x AMD Eng Sample: 100-000000504-04_34/21_N testing with a Supermicro H12DSG-O-CPU (2.1 BIOS) and ASPEED on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111268-HOWE-7773XGR31 2 x AMD Eng Sample: 100-000000504-04_34/21_N –…

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7713-gromacs Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a Inspur 4.02.06 and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111266-HOWE-7713GRO09 2 x AMD EPYC 7713 64-Core – ASPEED…

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Gromacs-m1pro Benchmarks – OpenBenchmarking.org

Apple M1 Pro testing with a Apple MacBook Pro and Apple M1 Pro on macOS 12.1 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111255-TJ-GROMACSM122 Apple M1 Pro – Apple M1 Pro – Apple…

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Gromacs: src/gromacs/options/optionfiletype.h File Reference

This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Defines an enumeration type for specifying file types for options. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com enum   gmx::OptionFileType {   eftUnknown, eftTopology, eftTrajectory, eftEnergy,   eftPDB, eftIndex, eftPlot, eftGenericData,   eftOptionFileType_NR }   Purpose of file(s) provided through an…

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HPC-AI Advisory Council Announces the Winners of the 4th APAC HPC-AI Competition

36 Student Teams from Around the Asia Pacific (APAC) Region Participated in the Six-Month Long Competition which included Training and Hands-on Challenges SINGAPORE & SUNNYVALE, Calif., November 18, 2021–(BUSINESS WIRE)–The HPC-AI Advisory Council (HPCAIAC) and National Supercomputing Centre (NSCC) Singapore today announced the university team winners of its annual HPC-AI…

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Gromacs: src/gromacs/mdtypes Directory Reference

Directory dependency graph for mdtypes: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   awh_correlation_history.h   file   awh_history.h   file   awh_params.h   file   commrec.h   file   df_history.cpp   file   df_history.h   file   edsamhistory.h   file…

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