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Questions related to Gromacs
I intend to write articles using experimental drilling data (inputs and outputs) for which I will need an appropriate analysis and prediction method. what is the chance of publishing an isi paper...
03 February 2023 1,041 2 View
Hi I have a martini system of 1642 atoms. Most of them are overlapping. I tried running energy minimization with all sorts of parameter manipulation but system doesn't resolve and crashes. I am...
25 January 2023 9,512 1 View
Dear Experts I need a list of specifications/components list for setting up a Desktop computer to do molecular dynamics simulation. The main purpose is to do Structure Based Drug Design and...
24 January 2023 9,090 3 View
I'm doing the simulation in single method as always. I haven't changed any parameters.
20 January 2023 4,104 0 View
What DFT method is the most accurate for calculating hydrogen bonding? Dispersion correction seems essential to large-system hydrogen bonds, whereas dispersion correction tends to overestimate...
05 January 2023 7,226 3 View
Hello, I need to build a polymer molecule for my molecular dynamics simulation. The target molecule is a random polymer composed of two monomers randomly connected with each other. I know...
14 December 2022 1,312 8 View
i am trying to do umbrella sampling of 2 AU molecules but whenever I am trying to run the md_pull.mdp file it giving an error : ERROR 1 [file md_pull.mdp]: When the maximum distance from a pull...
23 November 2022 1,285 1 View
There are 80 residues in your selected group dssp cmd='/usr/bin/dssp -i ddWL6jqm 2>/dev/null' Reading frame 0 time 0.000 Back Off! I just backed up ddWL6jqm to ./#ddWL6jqm.1#
22 November 2022 1,784 0 View
On what basis should the Ψ and φ values be selected
21 November 2022 992 1 View
Hi everyone, I need to perform MD simulations on a large number of protein-ligand docked complexes (88 or more). Previously, I used Swiss Param website to generate ligand topologies and CHARMM...
03 November 2022 8,540 2 View
Actually, it has been listed in here (https://charmm-gui.org/?doc=archive&lib=csml) with document named as toppar_all36_moreions.str but i could not find it. If anyone has, could you please...
26 October 2022 444 1 View
1. In preparing the MD simulation, an equilibration of about 100 ns is done. After building the pure lipid membrane from CHARMM-GUI, I have 6 equilibration.mdp files and one production.mdp file....
18 October 2022 9,899 4 View
Hello everyone! I want to calculate the polarizability of the ferroelectric phase, the phase transition barrier of my compound. Both at a fixed temperature and a heating process for simulation are...
16 October 2022 8,244 0 View
PatchDock online server for protein-peptide showed in result section: You have uploaded an empty file. The file is not empty inside, all the documents contains are PDB structure. How to solve this...
05 October 2022 3,428 3 View
Hello, I am trying to use PatchDock server. My receptor protein has the following structure: ATOM 1 N GLN 1 35.030 57.410 17.050 1.00 0.00 N ATOM 2 CA GLN...
29 September 2022 3,831 0 View
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 8,027 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 6,772 0 View
MM/PBSA is done for protein in the membrane system. Can anyone please suggest something?
10 June 2022 2,463 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 7,685 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 4,549 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 1,969 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 941 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 6,245 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 9,635 3 View