Tag: GROMACS
Does openMP respect LD_PRELOAD? – User discussions
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…
Gromacs: gmx::SimdDIBool Class Reference
#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…
Install on cray with mpi – User discussions
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,…
Position Restraining CNT during MD Production – User discussions
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…
[gmx-users] Xeon MP , DP
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…
Difference between potential mean force and free energy – User discussions
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,…
biochemistry – Need help with converting GROMACS topology to AMBER format for MMPBSA analysis
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 on cloud GPU – User discussions
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…
Protein+ATP+Mg complex Amber forcefield – User discussions
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 +…
A Beginner’s Guide to Perform Molecular Dynamics Simulation of a Membrane Protein using GROMACS — GROMACS tutorials https://tutorials.gromacs.org documentation
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…
ERROR No such moleculetype – User discussions
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…
Issue in convertion of pdb to gro file in the case of ligand – User discussions
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….
Why is the Flat Bottom Restraint Documentation so bad? – User discussions
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…
Placement of molecules in the corners of the simulation box. Why? – User discussions
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…
Free energy calculation of protein-ligand system – User discussions
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…
MDRUN crash during gREST simulation under NVT ensemble – User discussions
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…
Pull code distance restraint – User discussions
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…
Coarse-grained simulation of a nanocomposite with tables without particle decomposition – User discussions
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…
Protonating structures programmatically – User discussions
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…
Inclusion of electrostatic 1-4 interactions when exclusions nR are set at 3 – User discussions
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…
Protonation/disulfide issues with pdb2gmx? – User discussions
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…
Workshop: learn to code in GROMACS – Announcements
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…
Ligand moving out of the binding pocket – User discussions
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…
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…
Error Using gmx wham – User discussions
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…
Flat bottomed position restraints not working as intended – User discussions
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…
How to choose box length for lipid bilayer – User discussions
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…
Restraints of 2 different molecules in a simulation with different restraint spring constants – User discussions
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…
Zinc displacement and coordination – User discussions
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 researchers will get Microsoft Azure discount under NIH STRIDES program | University Times
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…
Error installing gromacs 2021.4 – User discussions
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…
Molecular Dynamics Software Market Share and Growth Latest Report [2023-2030]
PRESS RELEASE Published May 25, 2023 . Molecular Dynamics Software Market (2023) Report offers an in-depth analysis of the market status of the Molecular Dynamics Software Top manufacturers with definition, SWOT analysis, best facts and figures, PESTAL analysis, expert opinions, and the most recent developments worldwide. Molecular Dynamics Software Market…
Molecular Dynamics Software Market, Share, Growth, Trends And Forecast To 2030
A comprehensive research process that included primary as well as secondary information was used to create the global Molecular Dynamics Software market report. To collect qualitative and quantitative information about market trends, drivers, issues, and opportunities, primary research involves interviewing stakeholders, important opinion leaders, and industry experts. To verify the…
ABF error with colvars module – User discussions
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…
3 Tests Fail: MDRunIOTest – User discussions
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…
May 31st, Developer bi-weekly videoconference – Developers discussions
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…
Compiling GROMACS 2023 with Intel LLVM compilers – User discussions
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…
Structural basis of amine odorant perception by a mammal olfactory receptor
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)….
Implicit pore simulation – User discussions
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…
Periodic Boundary Conditions Error, Molecule Trajectory Collapses to 2D – User discussions
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
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> –…
xx of the yy bonded interactions could not be calculated gives different xx values with ddcheck and noddcheck
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…
Installation Issue with Python – User discussions
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,…
Mismatch between index file and tpr log – User discussions
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…
Distance b/w 2 group of atoms – User discussions
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…
“conserved energy” is not conserved – User discussions
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…
Getting index for clusters in system – User discussions
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…
Lipid parameters in KALP15-DPPC tutorial – User discussions
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…
Error when using a bash loop – User discussions
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…
Calculation of interaction energy between small molecules – User discussions
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…
Error while running writing the topology – User discussions
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…
BAR calculation – User discussions
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…
Gmx rms command – User discussions
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…
Low Performance due to low utilisation of GPU – User discussions
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…
Problem with H-bond – User discussions
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…
Gromacs: gmx::CommandLineProgramContext Class Reference
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,…
[ERROR] No default U-B types and Proper Dih. types – User discussions
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…
Using custom Fatty Acid to build bilayer – User discussions
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…
Non-bonded parameters in charmm36 forcefield – User discussions
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…
[gmx-users] about dumping the last frame
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…
Gmx rdf taking way too long reading frames – User discussions
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…
[GROMACS] How does the conformation obtained in the simulation remain stable in the next simulation? – User discussions
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…
Gromacs: src/gromacs/mdlib/groupcoord.h File Reference
#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…
Molecular Dynamics Simulation Software Industry 2023 Is Booming Across the Globe
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…
Holes in the membrane during equilibration – User discussions
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…
Lincs and electrostatics – User discussions
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…
Low performance and Thread-MPI error in multi GPU usage – User discussions
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…
Res ‘HIS’ is converted into ‘X’ after protonation – User discussions
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…
bash – Conflicts between Snakemake and GROMACS?
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…
How to apply Flat Bottom Position Restrains to 8 peptides – User discussions
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…
MdrunIOTests failed – User discussions
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…
Understanding Our World through GROMACS (Part I of II)
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…
Gromacs: src/gromacs/utility/include/gromacs/utility/path.h File Reference
#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 > …
Error in GB implicit solvent .tpr file generation – User discussions
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…
High Performance Computing Software Market size, share, trend | Complete Analysis
Report Description: The global High Performance Computing Software market analysis includes helpful information on both the global and local markets. The economy, results of value/volume, marketing strategy, and professional perspectives are all discussed. In addition, the research report includes data on product photographs, development, pricing, cost, specifications, capacity, market shares,…
Gromacs: src/gromacs/mdrunutility/multisim.cpp File Reference
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[],…
Forcefield error – User discussions
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…
Bioinformatics Software Market is set to experience a significant growth rate
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PhD Position in Structural Bioinformatics
We have the power of over 40,000 students and co-workers. Students who provide hope for the future. Co-workers who contribute to Linköping University meeting the challenges of the day. Our fundamental values rest on credibility, trust and security. By having the courage to think freely and innovate, our actions together,…
Protonation states using -inter – User discussions
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…
Molecular Dynamics Software Market to Witness Impressive Growth by 2030
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…
Constraining two water droplets at constant distance between their COMs using pull code – User discussions
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…
Ligand_ini.pdb is forming a distorted structure of ligand after running python script – User discussions
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…
How to choose when caculating rmsd – User discussions
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…
How to ensure solvent molecules are contiguous – User discussions
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…
Regression test failure – User discussions
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…
QM/MM CP2K + GROMACS Running mdrun error – User discussions
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 hangs when run from python multiprocess – User discussions
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…
Gromacs: gmx_nbnxn_ocl_t Struct Reference
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 with coordNum colvar in protein-lig binding SMD – User discussions
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…
Energy minimization gives broken resides – User discussions
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…
Gangle interactive index group selection, advance to next group – User discussions
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…
Gromacs: src/gromacs/trajectoryanalysis/modules Directory Reference
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…
Trjconv not writing chain identifiers anymore (since ca. v2019) – User discussions
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…
Combining structural waters with waters added by solvate – User discussions
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…
cudaStreamQuery failure – User discussions
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…
May 17th, Developer bi-weekly videoconference – Developers discussions
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…
Using steered MD to select near-native from decoys of docking models – User discussions
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…
Water box with a sheet of graphene – User discussions
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…
Test particle insertion problem – User discussions
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…