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Questions related to Gromacs
I have the ligand perimeter in my working folder and file but I am receiving an error in gromacs that says "Fatal error: Topology include file "ligand.prm" not found", how can I fix this, please....
15 February 2022 9,898 3 View
Dear Expertise, I want to ask, is there any software can find the similarities features between ligands/compounds? Thank you.
15 February 2022 3,589 4 View
Hello all. I am working on a ligand-dmso system using GROMACS. My system is supposed to be neutral but it is showing that it has an overall charge of 0.022153. I believe this is happening due to...
13 February 2022 8,080 3 View
I am trying to build a topology in GROMACS for NMA (N-methyl acetamide). I need to use one of the GROMOS force fields. I added my own rtp file to the force field for describing the NME residue,...
10 February 2022 2,487 2 View
I am seeking a way to obtain the contact map between two chains in a protein post MD simulation in gromacs. The objective is to analyze and know which residues in two chains are important during MD.
02 February 2022 574 3 View
I am using Gromacs 2020.1 on UBUNTU
31 January 2022 1,209 1 View
I am having 96 replicas of a system. I want to distribute the non-bonded calculations to GPUs and other calculations and update tasks in CPUs [outside the GPU...
21 January 2022 5,431 1 View
hello If the enzyme mutant contains mercury or chloride ligands in addition to the zinc ligand, Should zinc only be considered as a metal for simulation with Gromacs? Or must ligands such as...
14 January 2022 3,752 1 View
I follow the protein-ligand simulation tutorial protocol. For my own protein-ligand simulation, I give the following commands at the ion addition stage: gmx grompp -f ions.mdp -c solv.gro -p...
05 January 2022 9,312 1 View
I have done simulation of protein-ligand complex with gromacs version 2020.4. I need to do mmpbsa calculations. For that I try to install with gromacs 5.0 and 5.1 versions but nothing worked. What...
30 December 2021 9,371 2 View
Hello everyone, I have been trying to simulate a protein in water, but the following error appears: Fatal error: Too many LINCS warnings (1436) If you know what you are doing you can adjust the...
27 December 2021 4,030 2 View
Hello Gromacs developers and users, I’m dealing with a highly negative charged protein-RNA-ligand complex which happens to create a lot of problems with lots of counter ions being added to the...
22 December 2021 5,075 1 View
In gromacs while performing membrane protein simulations, it is taking much time to complete mdrun step as the protein system is huge, so I want to ask, is there a procedure which can be...
21 December 2021 1,734 2 View
I have a gromacs trajectory and I want to monitor the folding and stability of a certain helix in my protein, how can I do that? I tried to use DSSP through gromacs in version 2020.3, however on...
18 December 2021 7,948 3 View
I am trying to do an MD simulation of a peptide containing artificial amino acid (modified cysteine) and a linker as follows in Gromacs. I do not have forcefield parameters for these new molecule...
15 December 2021 8,350 5 View
I want to analyze the responses and conformational states of proteins at various temperatures in silico. Can I do this with molecular dynamics simulation programs like gromacs? Is there a special...
11 December 2021 7,483 3 View
Fatal error: Syntax error - File CHL.itp, line 7 Last line read:'[ atomtypes ] ' Invalid order for directive atomtypes. During the energy minimization step, I've obtained this error when I'm...
08 December 2021 1,537 3 View
Dear all I have few confusions about the pulling code in gromacs, I was using NAMD before and the method was quite straighforward in NAMD to pull the ligand out of the protein, in gromacs it is...
07 December 2021 466 1 View
how to create the coordinate and topology file for cyclohexane? And will all atomic simulation be possible?
01 December 2021 4,397 4 View
Hi all, I have several sets of MD runs and I would like to perform PCA analysis using Amber. I am quite a newbie with this package being mostly used to Gromacs/NAMD. In particular I would need to...
24 November 2021 4,498 5 View
I've a gromacs trajectory of 500 ns whose size after removing the solvent is about 2 GB. I want to generate a movie highlighting certain residues, I tried Chimera, it crashed and couldn't even...
21 November 2021 7,654 6 View
Dear all, I am doing simulation for a polymer/water system. I would like to do RDF and coordination number analysis for this system. I got results like in figure I attached here. I know the...
09 November 2021 9,112 3 View
Hello, I used gromacs 2020 and performed the 100ns simulation protein drug complex. I generated .tpr file for 100ns simulation using gromacs version 5 as g_mmpbsa works with gromacs 5x version...
02 November 2021 490 4 View
I am using Ubuntu 20.04 LTS on Windows 10. Problem is Ubuntu is not detecting any of my GPUs. I was working on Gromacs and when I tried to run simulations on GPU it said GPU not detected. Gromacs...
28 October 2021 7,309 4 View