Tag: GROMACS

lune June 8, 2023, 4:49pm 1 GROMACS version:2023.1GROMACS modification: No I’m currently profiling gromacs-2023.1 with CUDA acceleration. I’m trying to trace UVM page faults using NVIDIA nsight systems with a custom cudaMalloc shim library. It seems however, that GMX doesn’t interact with the CUDA API itself, and instead openMP forks…

#include <gromacs/simd/impl_reference/impl_reference_simd_double.h> Boolean type for integer datatypes corresponding to double SIMD. Available if GMX_SIMD_HAVE_DINT32_ARITHMETICS is 1. Note This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the…

GROMACS version: 2022.5GROMACS modification: No Hi, I would like to install gmx mpi for multidir simulations within a single node. Although it is not comparable, but it seems OK on my local box, but I fail to have a good build on our Cray. I use gnu prg env, gcc,…

GROMACS version: 2020.4GROMACS modification: NoHi,I want to position restrain the CNT during production. I have encountered following error Cannot find position restraint file restraint.gro (option -r). From gromacs-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as…

Post by Y. U. SasidharIs there a difference of performance between xeon MP and DP processorsrunning gromacs in single/ doble processor configurations ? I will haveto choose between MP and DP processors for a dual machine. I think the MP have larger cache but lower clock speeds. Go for DP…

fan June 8, 2023, 2:52pm 1 GROMACS version:GROMACS modification: Yes/NoHere post your question Dear Users, I used umbrella sampling and gmx WHAM to calculate the “free energy” of ions passing through a channel. In the literature [1], the free energy along the reaction coordinate is the potential mean force. However,…

Hello fellow researchers, I am currently facing an issue while performing an MMPBSA analysis over some AMBER topologies files converted from GROMACS. Specifically, I am working on a receptor system that contains a sodium ion (Na+) in a specific binding site, and my goal is to evaluate the binding energy…

GROMACS version: 2023 onwards into futureGROMACS modification: Yes/No Hi guys! I saw a little bit starting to appear online about Gromacs on cloud GPUs, incl gromacs’ paper from last year. So, I guess, some of you already started using cloud GPUs. Could you share any tips/insights? I am interested in…

satti June 7, 2023, 3:14pm 1 GROMACS version: 2023.1GROMACS modification: No Hello everyone, I have been doing simulations of a protein using AMBER99sb-ILDN using Gromacs. Now, I am planning to initiate simulations of a protein-ATP/ADP complex. While searching for ATP parameters I found a few papers which employed AMBER99sb*ILDN-parmbsc0-χOL3 +…

Building the protein-membrane system in CHARMM-GUI We are now ready to embed the protein structure in the membrane in the proper location and orientation and construct the membrane composition we desire. To do this, we utilized the CHARMM-GUI input Generator, a handy web-based tool to generate GROMACS inputs for the…

GROMACS version: 2020GROMACS modification: Noforcefield I am using: charmm36Here post your question: Hi,I ran grompp -f EM.mdp -c system.pdb -p system.top -o em.tpr and I got this error: ERROR 1 [file system_GMX_charmm36.top, line 22]: No such moleculetype sls * ——————————————————-Program: gmx grompp, version 2020Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2511) Fatal error:There…

GROMACS version:GROMACS modification: Yes/NoHere post your questionI got error in the conversion of pdb file of ligand to .gro file. I got a converted file but which is different from yours. When I compared your file with my file,the decimal spacing is mismatched. Glycine aRginine prOline Methionine Alanine Cystine Serine220jz4….

GROMACS version: 2023GROMACS modification: NoI am trying to understand how to set up a flat bottom potential and I have to admit, I am quite frustrated with the documentation. The restraint section:manual.gromacs.org/documentation/2023/reference-manual/functions/restraints.htmldoes not even mention, in which files the parameters are specified. But it does tell me I need to…

merry June 5, 2023, 9:06am 1 GROMACS version: 2019.4 Hi. I did 200 ns MD simulation for self assembly of a number of peptides.Why are my peptides placed in the corners of the box during the simulation??In the case of articles similar to my work, even in shorter times,I saw…

GROMACS version: 2021.4GROMACS modification: Yes (PLUMED patch) I am trying to calculate free energy of a system where one ligand molecule is stuck inside protein fibril and one outside the fibril. The inner ligand’s vdw force becomes zero and the outer becomes a non-zero value over lambda steps.I have tried…

GROMACS version: 2022.3GROMACS modification: No Hello everyone. I am currently using GROMACS ver. 2022.3 patched with PLUMED ver. 2.8.1., and I’ve been trying to replicate the gREST simulations from Oshima et al. (J. Chem. Inf. Model. 2020, 60, 11, 5382–5394) using GROMACS. In the paper, the authors perform gREST simulation…

GeoPou June 2, 2023, 12:37pm 1 GROMACS version:2022.5GROMACS modification: noHere post your question Hi, I want to simulate a protein-ligand system, and I would like to keep the small molecule within a certain distance from the protein. To do so, I would like to define centres of mass for the…

Yel21 June 2, 2023, 8:23am 1 Dear Gromacs users, We have an old coarse-grained polymer model with graphene (~ 3100 coarse-grained beads) that was built using the Inverse Boltzmann Iterative procedure with the help of VOTCA. This model is simulated without errors and warnings when gromacs 4.6.5 is employed with…

ga01 June 1, 2023, 8:31pm 1 GROMACS version: 21.5GROMACS modification: No Hi,I would like to ask for some advice on protonating residues when running simulations at pH values that are substantially different than neutral. Pdb2gmx has the -inter (and also -his, -lys, etc.) flags to set the protonation status of…

GROMACS version: 2022GROMACS modification: YesHi, I have a question about the inclusion of electrostatic charge-to-charge interactions in a topology. We are building our own force field and are using a custom modification to gromacs that allows for LJ 6-10 rather than 6-12. Our original intention was to use the force…

ga01 May 30, 2023, 7:22pm 1 GROMACS version: 2021.5GROMACS modification: NoHere post your question Dear GROMACS users,I would like to ask for some advice on file preparation and pdb2gmx. I plan to run simulations in higher than neutral pH, so I had to determine the correct protonation state of my…

Hi,The workshop “Learn to code in GROMACS” will be held 7- 8 September 2023 In Stockholm. The aim is to provide attendees with the basis for coding in GROMACS and contributing to the GROMACS developer community. We will have lectures, Q&A sessions, and hands-on sessions with mentoring covering the following…

NJ07 May 30, 2023, 4:32pm 1 GROMACS version: 5.1.4GROMACS modification: NoForefield: charmm36-jul2021Ligand topology from Swiss-Param Dear All, I am quite new to Gromacs and I need help with result analysis. I docked my ligand to the protein binding site and performed MD simulation for 50ns. However, I could see that…

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GROMACS version: 2018.3GROMACS modification: NoI have performed umbrella sampling simulation for the separation of carbon nanotubes in an organic solvent system.For the pmf calculation I am using gmx wham. But during the calculation I encountered the following error : Found 16 tpr and 16 pull force files in tpr-files.dat and…

GROMACS version: 2021.5GROMACS modification: No Hello I’m trying to simulate a system with 8 identical peptides and a lipidic membrane, but I want the peptides to interact with only one leaftlet of the membrane. I was told to use Flat-Bottomed position restraints to keep the peptides on one side. But…

mjm91 May 28, 2023, 11:46am 1 Dear gromacs users, I am working on a martini cg model of a mixed bilayer system. However I am a bit confused about choosing the correct box length using editconf. If I use gmx editconf -c -d 1.0 i.e. keeping 1 nm distance between…

roozi May 27, 2023, 2:16pm 1 GROMACS version: 2023GROMACS modification: No Dear All,I hae trouble defining using restraints with different restraint springs values for 2 diff molecules in my sim . I have generated the topology files using Charmm-Gui and then renamed restraint argument name in the topology file(.itp) of…

GROMACS version: 2023.1GROMACS modification: Yes/No Dear users,I have to deal with a simulation of a protein containing two zinc ions, tetrahedrally coordinated but with two different sets of ligands. In the first case, one zinc is bound by four cysteines residues – and I guess all of them should be…

Pitt has signed an agreement with Microsoft to participate in the NIH STRIDES (Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability) program, which will allow researchers to use Microsoft Azure at a 20 percent discount to support their NIH-funded research, according to Pitt IT. Pitt researchers with non-NIH…

GROMACS version: 2021.4GROMACS modification: Yes/No Hi, I am getting this error while installing gromacs 2021.4 please help me with it. I configured cmake as follows: cmake … -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_MPI=ON -DGMX_GPU=CUDA -DGMX_SIMD=AVX2_256 -DCMAKE_PREFIX_PATH=/usr/local/gromacs2021 -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2021 -DBUILD_SHARED_LIBS=ON -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.7 after this I am getting an error as follows: [ 92%] Building…

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GROMACS version:2022.5-Colvars_2023_05_01GROMACS modification: YesI am attempting to use ABF in the colvars module for my simulation. I have tried installing several versions of Gromacs (gromacs2021.6-colvars, fresh download of gromacs2022.5 that I patched with colvars). I have tried installing them on my own laptop in Ubuntu22.04 on WSL2 as well as…

GROMACS version: 2022.3, 2022.5, 2023.1GROMACS modification: NoHello, I’ve been having issues, trying all three of these GROMACS distributions. I’m running on an HPC, and I have included the basic error logs for the outputs of cmake and make check for the blank run after logging into the HPC. After gcc-7.5.0…

Dear GROMACS developers, Our next biweekly developer meeting will be on May 31st 17:00 (Stockholm time). At the moment we have three open slots, so if there’s anything you wish to discuss please let me or Berk know (or comment below)! Berk: general issues (open bugs, CI, maintenance) Open slot…

Erik May 24, 2023, 5:01pm 1 GROMACS version: 2023.1GROMACS modification: No I’m trying to compile GROMACS 2023 using Intel’s LLVM compilers and have run into a number of issues. The first is that they don’t seem to play nicely with nvcc because of a bug with the way nvcc sets…

Liberles, S. D. & Buck, L. B. A second class of chemosensory receptors in the olfactory epithelium. Nature 442, 645–650 (2006). Article  ADS  CAS  PubMed  Google Scholar  Buck, L. & Axel, R. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175–187 (1991)….

GROMACS version: 4.5/5/2021GROMACS modification: NoHere post your question : I am runing Go simulations and want to simulate protein entrance to a pore. The pore would be a cylinder that ends with a planar wall at z = 0. Thetransition between the cylindrical and planar wall would be modeled with…

GROMACS version: 2020.4GROMACS modification: No I have been running simulations of small proteins in water. Nothing fancy. Have been doing them without a hitch for awhile now. This last one I tried to do, however, behaved very strangely. The simulation seems to run for 125ns without any problems, but when…

gromacs-doc-2022.3-2.fc37 – Fedora Packages ↵ Return to the main page of gromacs-docView buildSearch for updates Package Info Changelog Provides Files Changelog Date Author Change 2022-09-28 Christoph Junghans <junghans at votca dot org> – 2022.3-2 – Rebuild for muparser 2022-09-02 Fedora Release Monitoring <release dash monitoring at fedoraproject dot org> –…

Summary In a topology with [ pairs ] between far atoms I get a fatal error when using domain decomposition. What I do not understand is why the error is different with or without -noddcheck without -noddchek Fatal error: 6896 of the 94640 bonded interactions could not be calculated because…

GROMACS version:2023.1GROMACS modification: NoHere post your question System: Ubuntu on WSL2 with Windows 11 I try to cmake gromacs using the following tags: cmake .. -DGMX_GPU=CUDA -DGMX_CUDA_TARGET_SM=”75″ -DGMX_CUDA_TARGET_COMPUTE=”75″ -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON -DGMX_PYTHON_PACKAGE=ON But the configure returns an error with the following statement: Traceback (most recent call last): File “<string>”, line 1,…

roozi May 21, 2023, 11:07pm 1 GROMACS version:2023GROMACS modification: No I have prepared an index file to be used in pull code . As i defined in make_ndex command there are 21 k atoms in one group and 12 k atoms in the 2nd group. but when i run grompp…

roozi May 20, 2023, 12:13pm 1 GROMACS version:2023GROMACS modification: No i am trying to compute dist. of 2 group of atoms in a single .gro file using the following command line script;gmx distance -f step4.gro -s topol.tpr -n index2.ndx -oall dist.xvg -select ‘com of group “gama” plus com of group…

GROMACS version: 2021.1GROMACS modification: Yes/No: NoHere post your question: I simulate a protein in vacuum (NVT ensemble) or in SPC/E water (NPT ensemble). dt = 1 fs, no constraints. I use a V-rescale thermostat and a Berendsen barostat. I am interested in the total energy exchange between the thermostat (and…

GROMACS version: 2021.2GROMACS modification: No After the simulation, I have gro file in which 7 clusters (micelles) are formed by surfactant molecules. I want to get the index of all the 7 clusters for post processing. I found that gmx clustsize -cut 0.7 option gives me correct number of clusters…

mjm91 May 19, 2023, 6:02am 1 Dear gromacs users, I have a question regarding the parameter inclusion of the berger lipids for the online gromacs tutorial of KALP15 in DPPC simulation. In the step for adding lipid topology or lipid.itp file (containing atomtypes, nonbonded parameters etc.), it is suggested that…

GROMACS version: 2022.4 GROMACS modification: No Hi, I am trying to use gromacs through a bash loop to automatically run through all my folders and sub-folders; and rename the output with the same of the folders and sub-folders. I have used this script on an external computer cluster through a…

GROMACS version: 2018.3GROMACS modification: NoMy system contains 512 ion pairs of Choline Chloride, 1024 EG, and 170 paracetamol molecules. I have calculated SR LJ and Coulomb energy between different energy groups. The SR LJ+Coul energy for different pairs are as follows: -12000 kJ/mol for paracetamol-paracetamol -17800 kJ/mol for choline chloride-paracetamol…

GROMACS version: 2023.1GROMACS modification: Yes/NoHere post your question I have one protein and ligand for simulation. am using charmm forcefield. when i run the command for topolgy generation: gmx pdb2gmx -f complex_aca.pdb -o protein_aca.gro -ter it showed the following error:Fatal error:The residues in the chain PCA1–LEU496 do not have a…

GROMACS version: module load gromacs/2020.2-cpuGROMACS modification: Yes/NoHere post your question Dear Gromacs Users, I hope that all is well. I have performed free energy transformations and in two cases I got in the Bennet Acceptance Ratio (BAR) calculation: “WARNING: Some of these results violate the Second Law of Thermodynamics:This is…

GROMACS version:GROMACS modification: Yes/No Hello all, I have a protein ligand complex trajectory, and I want to calculate the ligand RMSD after aligning the protein structure. My idea is that if I calculate ligand rmsd after fitting protein first, then if the ligand would be moving away then it would…

GROMACS version: 2023GROMACS modification: No My desktop has Intel(R) Core™ i9-10900K CPU @ 3.70GHz processor and Nvidia RTX 4090 GPU. This is gromacs version installed on my systemgmx –version GROMACS version: 2023Precision: mixedMemory model: 64 bitMPI library: thread_mpiOpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)GPU support: CUDANB cluster size: 8SIMD instructions: AVX2_256CPU…

GROMACS version: 2023.1GROMACS modification: Yes/NoHere post your question I have problem when i want calculate a H-bond Protein-Protein my cmd : gmx hbond -s md100.tpr -f md100_c.xtc -num hb100.xvg -tu ns -n index1.ndx the xvg file is like this : @TYPE xy@ view 0.15, 0.15, 0.75, 0.85@ legend on@ legend…

Program context implementation for command line programs. Constructors are provided mostly for unit testing purposes; in normal usage, a single CommandLineProgramContext object is constructed with initForCommandLine() in the beginning of the program. The returned object can be explicitly passed to other methods, or accessed through getProgramContext(). Unless explicitly noted otherwise,…

GROMACS version: gromacs/2021.4_cuda-11.4.3 [supercomputer]GROMACS modification: No Hello everyone! I am currently trying to the prepare protein-ligand complex. As I tried to do the grompp command, I’ve encountered 24 errors. [See below] I am using the latest CHARMM folder (jul2021) and have used the CGenFF in generating the .str file. I’d…

jjsci May 15, 2023, 5:05am 1 GROMACS version: 2022GROMACS modification: No Hi, I am trying to build an octanoic acid/octanoate bilayer. I have used cgenff to generate .itp files for both of these fatty acids but I am struggling understand how to incorporate them into the .rtp and .hbd files…

mjm91 May 13, 2023, 1:35pm 1 Hi everyone, I have a confusion regarding the charmm36 forcefield. Why are the charges present in the ffnonbonded.itp file are all zero? How can we reliably use charmm36 forcefields for a system with zero charge for any atom? Is there any other way they…

Post by nahren manuelDear Awasthi,go through GROMACS Introductory tutorial…trjconv -f abc.pdb -s abc.tpr -o 3frame.pdb -dump 3You can also open the pdb file in VMD and save only the last frameSIMPLE !nahrenFrom: Shirin Awasthi Subject: [gmx-users] about dumping the last frameTo: gmx-users at gromacs.orgDate: Monday, February 2, 2009, 12:00 PMHi.I…

jiji May 12, 2023, 9:25am 1 GROMACS version: 2021GROMACS modification: /NoHere post your question I have a trajectory files of 200 ns simulation of a system with 488007 atoms, around 20000 frames and it takes about 10-20 minutes to read one frame on my HPC environment of 1 GPU, 10…

Two chains and two ligands were put for simulation in the water system, and a conformation with low free energy was obtained through calculation, in which a ligand was attached to two bodies and bonded by hydrogen bonds. I hoped to put this conformation into another system (alcohol-water system) for…

#include <stdio.h>#include “gromacs/legacyheaders/typedefs.h”#include “gromacs/legacyheaders/types/commrec.h” Assemble atomic positions of a (small) subset of atoms and distribute to all nodes. This file contains functions to assemble the positions of a subset of the atoms and to do operations on it like determining the center of mass, or doing translations and rotations. These…

Global Molecular Dynamics Simulation Software market report has been planned by taking into account all the imperative parts of the market research that basically brings the market scene into core interest. CAGR value variance rate for the market, amid the estimated time can likewise be gotten with the Molecular Dynamics…

GROMACS version: 2021.3GROMACS modification: No Hi all, I created a Martini 2.2 PC/PE/CHOL membrane-protein system solvated in water, energy minimized the structure, ran a short NVT equilibration, and am equilibrating it at 1 bar and ~310 K conditions with 50 kJ/mol/nm position restraints on the protein to prevent deformation. I…

Hi all, I have a couple of questions; What is the purpose /advantage of having Lincs constraint on H bonds only, and why not other bonds? This is part of the NVE ensemble of the gromacs tutorialconstraint_algorithm = lincs ; holonomic constraintsconstraints = h-bonds; bonds involving H are constrained What…

GROMACS version: 2023.01GROMACS modification: No I installed GROMACS 2023.01 using the cmake command below. cmake … -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256 -DGMX_BUILD_MDRUN_ONLY=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DGMX_GPU=CUDA -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g+±9 But, When I execute mdrun like below,I got the error, THREAD_MPI is not complied during installation.mpirun -np 2 gmx mdrun -v -deffnm ${mini_prefix} -ntmpi…

GROMACS version:2022.2GROMACS modification: Yes/No@jalemkulI am using CHARMM36-mar2019 for Protein-Protein MD simulation.For the protonation of ‘HIS’ I am converting pdb into pqr using **pdb2pqr30** at pH=7.Next I’m assigning charges manually using command pdb2gmx -f xyz.pdb -o xyz.gro -water tip3p -ignh -merge all -ff charmm36-mar2019 -his. xyz.gro has HISD and HISE Residues…

I tried to simplify my issue as much as possible and still getting the error. The whole idea is that I want to execute (inside a much more complex workflow) the command: gmx mdrun -nt 12 -deffnm emin -cpi on a cluster. For that I have a conda environment with…

GROMACS version: 2021.5GROMACS modification: No Hello, I need to simulate the interaction of 8 identical peptides with a lipidic membrane. But I have to make sure they only interact with one monolayer, i.e I have to keep them in the upper half of the simulation box only with respect to…

jjose May 10, 2023, 12:26am 1 GROMACS version: 2023.1GROMACS modification: Nocmake is version 3.18.4 Installing GROMACS 2023.1 on Ubuntu, make check failed 1 test: MdrunIOTests.Runningctest -R MdrunIOTests –output-on-failure &> full_output.logyields a file, but I can’t upload it because I’m a “new user”, so perhaps I can upload it after making…

Thursday Aug 13, 2020 In Part I of two episodes about GROMACS, one of the world’s most widely used open source molecular dynamics (MD) applications, Erik Lindahl, Biophysics Professor at Stockholm University & KTH Royal Institute of Technology, and Roland Schulz, Parallel Software Engineer at Intel, unpack the mysteries of…

#include <filesystem>#include <string>#include <string_view>#include <utility>#include <vector> 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. Declares functions for OS-independent path handling. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com std::vector < std::filesystem::path > …

roozi May 9, 2023, 12:09am 1 GROMACS version:2018.8GROMACS modification: No Hi there,I got an error message when running grompp for gb implicit solvent model :Fatal error:Can’t do GB electrostatics; the implicit_genborn_params section of theforcefield is missing parameters for 31 atomtypes or they might be negative.i have used Charmm36m FF for…

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void  gmx_sumd_sim (int nr, double r[], const gmx_multisim_t *ms)   Calculate the sum over the simulations of an array of doubles.   void  gmx_sumf_sim (int nr, float r[], const gmx_multisim_t *ms)   Calculate the sum over the simulations of an array of floats.   void  gmx_sumi_sim (int nr, int r[],…

GROMACS version:2018.1-1GROMACS modification: Yes/NoHere post your questionhelloi have done 3 to 4 simulation on gromacs and gives good results. but now i am trying to increase the the ns so its show error when I apply every force field. i have checked it on other than my protein and the…

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GROMACS version: 2020.4GROMACS modification: no If I want my protein residues to be in the default protonation states in physiological pH, for example, Lysine +1, Glutamine (0), Glutamic acid (-1), and so on … should I skip the -inter flag at the beginning while doing pdb2gmx? and just generate the…

The global Molecular Dynamics Software market research report is focuses on an overall consumption pattern, development trends, sales patterns and sales in key countries of the Molecular Dynamics Software market. The report focuses on global Molecular Dynamics Software vendors, marketing department and competition. This report also provides a detailed information…

GROMACS version: 2021.3GROMACS modification: No Hello all, I need to constrain two water droplets, each having 5000 molecules with different residue names (SOL1 and SOL2) and atom names. I have recently tried pull code with the following MDP options: pull = yespull_ngroups = 2pull_ncoords = 1pull_group1_name = SOL1pull_group2_name = SOL2pull_coord1_type…

Amey May 3, 2023, 10:42am 1 GROMACS version:2022.4Dear all,I am Trying to run ligand-protein complex MD simulation in GROMACS. My ligand_ini.pdb and ligand.gro files are not generating properly.After running of python script downloaded from MacKerell lab website a file is generated: ligand_ini.pdb. After viewing it in VMD it does not…

GROMACS version:2023GROMACS modification: Yes/No Hello everyone,I am new to gromacs and trying to generate a rmsd curve from gromacs for the Protein-ligand complex which could be similar to the schroedinger plot. But I am very comfused about how to choose group for the command gmx rms. this is the reference…

GROMACS version: 2023GROMACS modification: No I am preparing a system in which I am including structural waters, and also adding waters using solvate. In my starting pdb the structural waters are in a separate chain, which comes last after some polypeptide chains. After solvate, structural waters appear in the coordinate…

GROMACS version 2023.1 Dear GROMACS forum I having an issue with the regression tests following a test install of GROMACS 2023.1 on Ubuntu 22.04.02 LTS on a basic desktop. The installation step has worked without a hitch the output from gmx mdrun -version is pasted below. During the regression tests…

GROMACS version: 2023.1GROMACS modification: No Dear GROMACS community I have been trying to run QM/MM calculations using the CP2K interface in GROMACS.I have compiled the codes in multiple occasions, using different configurations. CP2K 2023.1: using Eiger arch file, using full toolchain installation (-install all), using other variations: fftw=install –with-plumed=no –with-sirius=no…

GROMACS version: 2022.4GROMACS modification: NoHere post your question Dear all,I have written a small python program that runs multiple simulations under Linux using multiprocessing to run a set of parallel simulations. The program then analises the data from each produced trajectory.Each thread runs a single instance of gmx and produces…

Public Attributes const gmx_device_info_t *  dev_info   OpenCL device information.   struct gmx_device_runtime_data_t *  dev_rundata   OpenCL runtime data (context, kernels) More…   cl_kernel  kernel_pruneonly [ePruneNR]   prune kernels, ePruneKind defined the kernel kinds   bool  bPrefetchLjParam   true if prefetching fg i-atom LJ parameters should be used in the…

GROMACS version: Gromacs 2021 with colvarsGROMACS modification: YesI am trying to run an SMD using ‘coordNum’ colvar to slowly increase number of contacts between protein and ligand. Following is my “colvar.dat” to run using “gmx mdrun -s smd.tpr -deffnm smd -colvars colvar.dat” The simulation runs but the first step itself…

GROMACS version: 2022GROMACS modification: NoHere post your questionI tried to minimized the structure obtained from Modeller.Here is the min.mdp: cpp = /lib/cpp;define = -DFLEXIBLEconstraints = noneintegrator = steepnsteps = -1;; Energy minimizing stuff;emtol = 500emstep = 0.001 nstcomm = 1ns_type = gridrlist = 1rcoulomb = 1.0rvdw = 1.0Tcoupl = noPcoupl…

aheim April 28, 2023, 2:55pm 1 GROMACS version: 2022-3GROMACS modification: YesA low priority question since I have a workaround but:I too am attempting to measure the angle between rings. I’d like to use the -n option and select index groups interactively instead of using the selection syntax in the -group1/2…

Directory dependency graph for modules: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   angle.cpp   file   angle.h   file   distance.cpp   file   distance.h   file   freevolume.cpp   file   freevolume.h   file   pairdist.cpp   file…

vedat April 28, 2023, 10:07am 1 GROMACS version: 2023.1GROMACS modification: Yes/No (required!) Hi guys, this question is addressing the Gromacs developers. Gromacs v2018.7 as the last version I’m aware of was able to write chain identifiers into a PDB file extracted from an XTC trajectory and using as topology (with…

RomanS April 28, 2023, 2:26pm 1 GROMACS version: 2023GROMACS modification: No I would like to retain some waters from the solved structure I am using to set up my simulation and combine them with solvent waters added by solvate. As Justin pointed out to me here, doing this naively is…

GROMACS version: 2023.1GROMACS modification: No Hi everyone,I am running some benchmarks (82k atoms, protein in membrane surrounded by water, 2 fs time step) and some systems of interest using “gmx mdrun -s benchMEM.tpr -v -nsteps -1 -maxh 1.0 -resethway” calculation starts running well after a couple of minutes I got:…Running…

hess April 27, 2023, 12:57pm 1 Dear GROMACS developers, On Wednesday May 17th at 17:00 we will have our biweekly developer call. At the moment we have two open slots. If there’s anything you wish to discuss, just let me know. Berk: general issues (open bugs, CI, maintenance) Berk: MDModules…

GROMACS version: 2022.3GROMACS modification: Yes/No Hello, I wish to use steered MD to select near-native antibody-antigen docking pose from a bunch of decoy docking poses generated using ZDock.My assumption is that the near-native structure would bind stronger than the decoys, and either the energy / force used to dissociate the…

GROMACS version: 2020.1-Ubuntu-2020.1-1GROMACS modification: No Hello everybody.I am trying to create a box with a sheet of graphene solvated with H2O, with a size of 17.09 x 25 x 27.13 (angstrom). The system preparation parameters are: rlis = rcoulomb = rvdw = 0.6 System optimization normally occurs with grompp and…

GROMACS version: 2020.4 (mpi version)GROMACS modification: NoHere post your question I am trying to follow the TPI tutorial here: Test particle insertion – GASERI So I prepare a tpi.top file with the topology as listed on the page to indicate the insertion of one atom (CH4-type atom). Then I run…