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Questions related to Gromacs
Water content in IPA is 1.7%. I want to decrease it to less than 0.5%. I have tried simple distillation and also distillation using an entertainer such as ethylene glycol. No positive results were...
10 August 2022 8,182 7 View
Hello expert, I had run my sample (DNA-small molecule) for 50ns. Unfortunately, before it complete, I have electrical problem and my run was stopped. Later, I mistakenly took the wrong md.tpr...
21 July 2022 6,954 0 View
MM/PBSA is done for protein in the membrane system. Can anyone please suggest something?
10 June 2022 2,595 1 View
I have run the production step for a protein-membrane system using Gromacs. But, the relevant stepX.X_production.xtc has not generated so that I can't proceed to the RMSD analysis. How can I fix...
31 May 2022 7,838 3 View
I tried to predict the structure of protein complex by alphafold2 using AlphaFold2_complexes (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2_complexes.ipynb) To...
19 May 2022 4,699 0 View
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 2,109 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 1,101 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 6,403 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 9,793 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 10,046 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 3,779 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 8,257 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 2,657 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 742 3 View
I am using Gromacs 2020.1 on UBUNTU
31 January 2022 1,337 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 5,565 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 3,891 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 9,483 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 9,489 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 4,165 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 5,205 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 1,873 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 8,109 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 8,500 5 View