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Questions related to Gromacs
Hello everyone! Can anyone please help me out in plotting an energy graph in gromacs, the problem is that I've simulated my system for 1 microsecond and since at every 2 pico second the output is...
11 May 2022 2,026 4 View
I need .gro, .itp, and .prm file for heteroatom for simulations of TM-proteins. Automated Topology Builder is not generating these files. Similar is the case with PRODRG? Any suggestions please.
23 April 2022 1,008 4 View
i want use the g_density3Darea in my work, but when i compile it use the command: gcc g_density3Darea follow the error: g_density3Darea.c:37:10: fatal error: sysstuff.h: No such file or...
17 March 2022 6,295 5 View
Dear Members, I am planning to buy a PC with the following configuration- Processor- 10th Gen Intel® Core™ i9-10900 (20 MB cache, 10 cores, 20 threads, 2.80 to 5.20 GHz Turbo, 65W) Memory- 32 GB...
10 March 2022 9,679 3 View
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 9,966 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 3,665 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 8,142 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 2,538 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 647 3 View
I am using Gromacs 2020.1 on UBUNTU
31 January 2022 1,255 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 5,487 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 3,816 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 9,373 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 9,413 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 4,073 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 5,133 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 1,797 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 8,013 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 8,404 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 7,536 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 1,597 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 549 1 View
how to create the coordinate and topology file for cyclohexane? And will all atomic simulation be possible?
01 December 2021 4,458 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 4,556 5 View