Tag: grompp

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: 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…

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…

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: 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…

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…

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: 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…

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…

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,…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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:…

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…

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…

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…

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…

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?…

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,…

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…

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….

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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:…

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…

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…