Tag: grompp

Scaling of MD with domain decomposition on JUWELS Cluster – Developers discussions

GROMACS version: 2024-dev-20240201-787d96c7a9-unknownGROMACS modification: YesI’m conducting some performance tests on the JUWELS Cluster, trying to see the improvement in performance that DD can bring within a single node. GROMACS build infoHere, GROMACS was built using GCC v11.4.0, uses OpenMP and OpenMPI v4.1.5, and builds its own FFTW v3.3.8. JUWELS Cluster…

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Lipid vesicle(CHARMM Gui files) simulation in GROMACS – User discussions

GROMACS version: 2022.1 and 2020GROMACS modification: Yes/NoHere post your questionHello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly….

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Command to run gromacs in parallel – User discussions

cjbraz December 11, 2023, 5:06pm 1 GROMACS version: 2023.2GROMACS modification: Yes/NoHere post your question Hello all. I have used CHARMM-GUI solvent builder to print out a script I can use in a protein simulation. I am able to run the script successfully, but would like to run the full script…

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Atomtype not found but it is defined in forcefield files – User discussions

Wang December 5, 2023, 1:57pm 1 GROMACS version: 2019.4GROMACS modification: YesHi, I was trying to add ions to a protein mixture system using grompp but got an error concerning the top file stating that atomtype NH3 (referring to the first residue of the protein) was not found. However, NH3 as…

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Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions

sam13 November 27, 2023, 12:33am 1 GROMACS version: 🙂 GROMACS – gmx grompp, 2023.3-Homebrew (-:GROMACS modification: No Hello,I have been trying to do MD simulation for a protein whose 3D structure is predicted by AlphaFold. The ligand is Aspartate molecule. I am following a similar approach to the Protein-Ligand GROMACS…

Continue Reading Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions

Error found during the production run – User discussions

Loknath November 18, 2023, 9:43am 1 After equilibration, I increased the box length for the air-water interface simulation but I got error as below“There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 6.24938 nmChange the number of ranks…

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[ atomtypes ] error – User discussions

GROMACS version:GROMACS modification: Yes/NoI want to simulate two types of small molecules in the system, and each type there are multiple of them.I created the files.itp for ligand1 and ligand2 Acpype Server serverThe question I have is this: since there are two types of molecules, can I have two itp…

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Reduce PDB doesn’t match Topology File atom – User discussions

GROMACS version: 2023.2GROMACS modification: No I am testing running proteins with mutations through AlphaFold and then passing the PDBs to gromacs to run relaxation. I originally attempted to run this without reducing the molecule, but that definitely didn’t work. Next, I reduced the structure using GitHub – rlabduke/reduce: Reduce –…

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Generating ion.tpr file – User discussions

AF1 November 1, 2023, 11:49am 1 Hi I am getting the following error from Lysozyme in water tutorial. I successfully completed this tutorial a few months ago but this week it seems the file gets broken at the ions.tpr output step. Please see message and file generated. Command line:gmx grompp…

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Mdout.mdp files on Gromacs – User discussions

Nik October 30, 2023, 4:22pm 1 GROMACS version: 2023.1GROMACS modification: NoWhy when I run equilibration in Gromacs an mdout.mdp file is generated? I use my my own nvt.md and npt.md files as the input ones (parametrs in files specified for Charmm force field as listed in Gromacs documentation. Does it…

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Running repeats during production run and restarting them – User discussions

GROMACS version: 2022.3GROMACS modification: No I want to run repeats starting from the end of my equilibration run. I saw on a tutorial that I can and should generate new velocities so I currently have gen-vel = yes and gen-seed = -1 for each repeat. However, since I am generating…

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GMX_MPI running – User discussions

Hi everyone!I have some problems with running gmx_mpi on more then one nodes. I have 4 nodes to run with 64 threads, but when i use slurm script with “mpirun gmx_mpi …”, gromacs starts the process on 4 nodes with… 32 cores in total, when 4 nodes will be with…

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gromacs 2023.3 – Download, Browsing & More

gromacs 2023.3 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2023.3.tar.gz (19 Oct 10:41, 42071770 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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Issue with covalent protein-ligand model/Adding ions step – User discussions

GROMACS version: gmx grompp, version 2023-openSUSEGROMACS modification: Yes/NoHi all, I am working on my covalent ligand-protein model (Cys-ligand) and adding Cys-ligand as a new residue to FF (charmm36-jul2022.ff). I got an issue using gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Generated 167799 of the 167910 non-bonded parameter…

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How to continue a simulation when suddenly stopped? – User discussions

nhina October 11, 2023, 4:56pm 1 GROMACS version:2019GROMACS modification: Yes/NoHi everyone,I’m running .sh file like below and the simulation is stopped at step 100300. How should I change the command to restore simulation from step 100300 without having to rerun from step 1? “for ((i=0;i<=1;i=i+1))dogmx grompp -f nvt.mdp -r em.gro…

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Fatal Error: Too many warnings (1) Use -maxwarn option in gromacs 2023.2 – User discussions

Respected Sir/Ma’am,I am getting an error as shown below.🙂 GROMACS – gmx grompp, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmxData prefix: /usr/local/gromacsWorking dir: /home/drr-18/Complex_02_EMinimizedCommand line:gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr Ignoring obsolete mdp entry ‘title’Ignoring obsolete mdp entry ‘ns_type’ WARNING 1 [file npt.mdp]:The…

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Position restraints with arbitrary reference positions? – User discussions

zauhar September 26, 2023, 4:03pm 1 GROMACS version: 2023GROMACS modification: No Hi, I want to define position restraints for selected atoms, where the reference position is an arbitrary coordinate. All the examples I see are to restraint atoms to their initial positions. Is there a file format to explicitly specify…

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Assertion failed error in Gromacs during NVT equilibration in Protein-Ligand Complex tutorial? – User discussions

GROMACS version:2022GROMACS modification: Yes/NoI am trying to perform simulation on my protein-ligand complex following Gromacs Protein-Ligand complex tutorial, during NVT equilibration using the command“gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr “i encountered an error“Assertion failed:Condition: ip.conctr.dA > 0We should only have positive constraint…

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Issue with modified residues and compressed-x-grps – User discussions

Solly September 6, 2023, 6:13am 1 GROMACS version: 2022.3GROMACS modification: NoDear users and developers of GROMACS! I want to report a small problem that I had recently with recording the trajectory of my simulation.I have GROMACS 2022 on my laptop and on a computing server. On the personal computer I…

Continue Reading Issue with modified residues and compressed-x-grps – User discussions

Npt Equilibiration Error – User discussions

below is the code and the output.gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr🙂 GROMACS – gmx grompp, 2022.4 (-: Executable: /usr/local/gromacs/bin/gmxData prefix: /usr/local/gromacsWorking dir: /home/aqsakhalid/Documents/MD_simulation/MSP_simulationCommand line:gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr…

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Using tool of charmm2gmx – User discussions

Brief description of tools/files:Charmm2gmx 1.0.2J. Chem. Inf. Model. 2023, 63, 14, 4246–4252awacha.gitlab.io/charmm2gmx/index.html Link:Contact person (JieChen and chenjiedlpu@163.com): How the work has been tested/reviewed:Hi Proffessor Justin, I found good tool for convert CHARMM stream files produced by CGenFF to GROMACS topologies, named Charmm2gmx. It likes the python file of charmm2gmx.py. But…

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Dihedral Mutiplicity cannot be perturbed – User discussions

oSalad August 23, 2023, 6:21am 1 GROMACS version: 2021GROMACS modification: No Hello,I am trying to run FEP on a molecule to convert it from a protonated to an unprotonated form. When running grompp, I initially got the error:ERROR 1 [file pap2.itp, line 140]:Proper Dih. multiplicity can not be perturbed 2.000000!=4.000000…

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System blows up when restarting with Martini3-Go? – User discussions

GROMACS version: 2022.1GROMACS modification: No I can get a multi-microsecond run with my system (Martini3, Go model). For this setup, I have several virtual beads that overlap with other beads, but I define exclusion between the overlapping beads in my topology file. Everything looks good in my initial run, but…

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Error assembling .tpr file from .mdp file for energy minimization (solved) – User discussions

GROMACS version: 2023.2GROMACS modification: Nodevice: M1 macbook (arm not intel) Hi everyone, I have been following this tutorial from Virginia Tech and ran into an error at the energy minimization step. After downloading the MDP file minum.mdp and adding it to my directory that I have been using so far…

Continue Reading Error assembling .tpr file from .mdp file for energy minimization (solved) – User discussions

Protein-Ligand complex MD simulation – User discussions

GROMACS version: 2020GROMACS modification: Yes/NoHere post your question I have been attempting to do a Protein-Ligand simulation and ran into an error. I converted the pdb file of the protein to generate a .gro file, a itp (posre) file, and a topol.top file. I used LigParGen to create the .itp…

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Difficulty in generating ION.tpr file using AMBER01 FF and SPC water model – User discussions

GROMACS version:2022.5GROMACS modification: Yes/NoHere post your question: During performing the MD Simulation of pdb:4xkx in GROMACS 2022.5. We selected AMBER03 Force Field & SPC Water model It is showing error during generating ION.tpr file ERROR IS: (base) master01@master01-HP-Z640-Workstation:~/Desktop/MD_GROMACS/MD_GROMACS_6$ gmx grompp -f ions.mdp -c box_sol.gro -p topol.top -o ION.tpr🙂 GROMACS –…

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PP computation – User discussions

GROMACS version: 2021GROMACS modification: No Hi, I am trying to compare the performance of GROMACS in two different high performance computers for which I am obtaining very big differences in computational times for different number of nodes (I am not using GPUs yet): around 15 times slower in every case.For…

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gromacs 2023.2 – Download, Browsing & More

gromacs 2023.2 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2023.2.tar.gz (12 Jul 16:21, 41930578 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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ARM 23.04 compilers generate incorrect code for GROMACS from -02 – High Performance Computing (HPC) forum – Support forums

I faced several issues when using the latest ARM 23.04.1 compilers with GROMACS on Fugaku (aka A64fx aka SVE 512bits) This is the most problematic one. FWIW ARM compilers 23.1 works great, and even with -Ofast The issue can be evidenced with the latest GROMACS 2023.1 and the regression test…

Continue Reading ARM 23.04 compilers generate incorrect code for GROMACS from -02 – High Performance Computing (HPC) forum – Support forums

Problems trying to add ions – User discussions

GROMACS version: 2023.1GROMACS modification:No Hiim trying to run this line:gmx_mpi grompp -f ions.mdp -c beta_solvated.gro -p topol.top -o beta_pp_ionize.tpr And the following error comes up. I don’t understand why, of course there a charge, that’s why I want to add ions.I’m using amber99sb-ildn FF.Thanks! Ignoring obsolete mdp entry ‘ns_type’Setting the…

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GROMACS Tutorial: Coarse-Grained Simulations with Martini 3 Force Field

  In today’s blog post, we’re going to explore an interesting technique called coarse-grained (CG) simulation and we are going to see how to run them using GROMACS. Specifically, we’ll focus on the Martini force field, which is rapidly gaining popularity to perform CG simulations of biomolecular systems. In this…

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GROMOS54a7 ff leads to missing parameters in topology after S-S-bonds between Cys residues were app – User discussions

GROMACS version: gromacs-2021.6GROMACS modification: No Hello community! I am a relatively new GROMACS user, who worked with GROMACS during my bachelor’s thesis – but being supported by a PHD student a few years ago already. Now I am working with GROMACS again to obtain results for my Master Thesis but…

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How to solve No default Improper Dih. types – User discussions

GROMACS version:2023.1GROMACS modification: Yes/NoHere post your questionI am using gromacs to run a simulation for glibenclamide as a ligand and ATP-sensitive potassium channel protein, however i am keep getting the error due to No default Improper Dih. typeshow I can solve the issue?below is the command the output messagegmx grompp…

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Performing Simulation for Begginer – User discussions

umar June 23, 2023, 5:02am 1 GROMACS version: 2023.1GROMACS modification: Yes/No Hello.I am new student of MD simulation and I started by learning 1aki (Lysozyme in water) simulation tutorial. Now I was given assignment of performing simulation of small molecules eg 90 molecules of 1-propanol in 10 water molecules. Here…

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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…

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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…

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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….

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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…

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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…

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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…

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[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…

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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…

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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…

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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…

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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…

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use a script run by gromacs to analysis protein protein complex dynamic – kehan

using gromacs to write a script for protein-protein complex moleculer dynamics from force field selection to trajectory analyze step by step,and give annotation to each line GROMACS is a powerful molecular dynamics software package used for simulating complex biomolecular systems. Below is a step-by-step example of preparing and running a protein-protein complex simulation…

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Regarding nvt file of protein-complex – User discussions

GROMACS version:GROMACS modification: Yes/NoHere post your question ERROR 1 [file topol_1.top, line 121]:Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =77, while at->nr = 77) Program: gmx grompp, version 2019.4Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1244) Fatal error:There was 1 error in input file(s) Karis April 20, 2023,…

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Unknown cmap torsion between atoms near modified residue – User discussions

GROMACS version: 5.1.4 2020GROMACS modification: Yes/No I’m simulating a single protein with phosphorylated serine-modified amino acid. I’m using charm36-mar2019 ff.Earlier while converting pdb2gmx the input file showed fatal error many times:“Residue 34 named GLY of a molecule in the input file was mapped to an entry in the topology database,…

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Cannot compile tpr file for CP2K QM/MM simulation with constraints = h-bonds – User discussions

AlbinP April 17, 2023, 5:16am 1 GROMACS version: 2022.5 with CP2K 2023.1GROMACS modification: No While running grompp to create a tpr file for QM/MM simulation below warning regarding constraints is displayed.WARNING 1 [file qmmm.mdp]:Your QM subsystem has a lot of constrained bonds. They probably have beengenerated automatically. That could produce…

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Gromacs+CP2K, cannot find atomic number – User discussions

GROMACS version:2023GROMACS modification: NoForce filed: Amber99SB-ildn, GAFFCP2K version: 2023.1 Protein-ligand system, want to use QM for ligand and contacting residue, MM for the rest. Command: gmx grompp -f md_qmmm.mdp -c md.gro -p topol.top -o md_qmmm.tpr -n index.ndxMsg prompting: Program: gmx grompp, version 2023-EasyBuild_4.7.2.dev0_r5ec768ef07c86f5c99d1670192971a80bd72412fSource file: src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp (line 282) Fatal error:Atoms 6126…

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Awh mdp options – User discussions

Gmx_QA April 14, 2023, 11:04am 1 GROMACS version: 2021.5GROMACS modification: No Hi! I am trying the seemingly simple task of pulling a molecule through a bilayer using the pull-code + awh, but I am confused about some of the options, and how they influence each other. The initial setup I…

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How to get maximum efficiency for GROMACS GPU calculation – User discussions

GROMACS version:GROMACS 2020.4-GPUGROMACS modification: Yes/No Hi,I am new for GROMACS, and doing 100ps NVT equilibration of a glycated SARS-CoV2 spike protein in explicit water (total number of atoms 674050). Below is my bash script: #!/bin/csh#SBATCH -o slurm.%N.%j.out#SBATCH -e slurm.%N.%j.err#SBATCH -p dhvi-md-gpu#SBATCH –gres=gpu:1 module load GROMACS/2020-4-GPU gmx_mod grompp -f eq_nvt-SARS.mdp -c…

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How do I pass .itp position restraints to grompp? – User discussions

GROMACS version: 2023GROMACS modification: No Hi everyone, this is my first time posting here 🙂 I downloaded gromacs 2023 today and I’ve been going through the tutorial I found here: Lysozyme in Water In the first step of the tutorial, we use pdb2gmx to produce the topology, position restraint, and…

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Parrinello-Rahman instability in Gromacs 2023 – User discussions

GROMACS version:2023GROMACS modification: No Hello everyone!Recently i’ve moved to Gromacs 2023 and really happy about it’s performance. But occasionally, it happens to segfault on simulations in N.-H. & P.-R. NPT of one of my systems. It warns with “Pressure scaling more than 1%”, despite system is seems to be well…

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Qmmm, gromacs+cp2k – User discussions

Samuel March 9, 2023, 7:17pm 1 GROMACS version: 2022.5GROMACS modification: Yes/NoHere post your question “Fatal error: Atoms 4682 does not have atomic number needed for QMMM. Check atomtypes section in your topology or forcefield.” I am performing a hybrid QMMM molecular dynamics simulation of a protein and ligand. When running…

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Invalid T coupling input: 3 groups, 2 ref-t values and 2 tau-t values – User discussions

GROMACS version: 2023GROMACS modification: Yes/NoHere post your questionFatal error:Invalid T coupling input: 3 groups, 2 ref-t values and 2 tau-t valuesby this command gmx grompp -f nvt.mdp -c em.gro -r em. gro -p topol.top -n index.ndx -o nvt.tprI done all staps relatesd to equlibrum but this error i can not…

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Density mediated simulation fine refinement – User discussions

dave March 2, 2023, 7:50am 1 GROMACS version: gromacs-2022.2GROMACS modification: No Hi All,(maybe more relevant to Dr. Christian Blau) It has been long I did not do MD simulations. I came across an old Bioexcel webinar about density mediated simulation by Christian Blau. It seems to be a very helpful…

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Mdrun speed is very low – User discussions

pulkit February 22, 2023, 12:45pm 1 GROMACS version:GROMACS modification: Yes/NoHere post your questiondear gromacs users and developers these are my commands (below) for running simulaion. the simulation is running very slow. can anyone please suggest the reason and possible solution of this problem. architecture of installaiongmx_mpi mdrun -version GROMACS version:…

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Gromacs not maintaining the bond angles of arginine during energy minimization – User discussions

PanyueW February 14, 2023, 2:58am 1 GROMACS version: 2022.1GROMACS modification: NoI am trying to run MD using a neutral system where all charged residues are neutralized. For example, I will have deprotonated arginines in my protein. I am not able to maintain bond angles of arginine residues when running energy…

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gromacs 2023 – Download, Browsing & More

gromacs 2023 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2023.tar.gz (6 Feb 19:24, 41863526 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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Overriding Proper Dih. parameters – User discussions

GROMACS version: VERSION 5.1.1GROMACS modification: Yes/NoHere post your questionDear experts,While using ions.tpr command line I am facing errors. Forcefield used: charmm36-mar2019.ffCommand line:gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry ‘title’ Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# NOTE 1 [file ions.mdp]:With Verlet…

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Syntax error – File UNL.itp, line 6 Last line read: ‘[ atomtypes ]’ Invalid order for directive atom – User discussions

GROMACS version:GROMACS modification: Yes/NoHere post your questionwhile running the following command:gmx grompp -f ions.mdp -c 1_solvated.gro -p topol.top -o ions.tprI am getting this:Fatal error:Syntax error – File UNL.itp, line 6Last line read:‘[ atomtypes ]’Invalid order for directive atomtypesLink for documents:drive.google.com/drive/folders/1Ka4B4DVvsRMexdsMOqw13GXadev0TTNO?usp=sharing HI,It looks like that the order of the directives in…

Continue Reading Syntax error – File UNL.itp, line 6 Last line read: ‘[ atomtypes ]’ Invalid order for directive atom – User discussions

Removing the all intramolecular interaction for solute molecule Or just freezing solute – User discussions

pinoji1 January 6, 2023, 10:23pm #1 GROMACS version:GROMACS modification: NoHow do I remove all forces (bond stretch, bending, dihedral, LJ occurs internally etc.) for one solute molecule while keeping the LJ interaction on for solute and solvent molecule?And related question What does following line (in [moleculatype] section) does to simulation?…

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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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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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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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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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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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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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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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[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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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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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] 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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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] 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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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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Tau t gromacs manual

Tau t gromacs manual TAU at TACC – TACC User PortalBiomolecules | Free Full-Text | Electrostatics of Tau GN Drive Tau | The Gundam Wiki | Fandom Kirk took a break and sent out for coffee when a patrolman brought him…

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Queries regarding temperature gradient

Post by Sabreen FarnazDear all,This is in regard to my previous queries. The warning in NVT step canpossibly be ignored using -maxwarn but I am still not sure about the rest!Can someone please help? tau_t = -1 means temperature coupling is not applied. Whether that’swhat you want or not is…

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