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I am running final md simulation for 100ns , after 7ns run , showing too many lincs warning , Here is my md.mdp file. title = OPLS Lysozyme NPT equilibration ; Run...
08 March 2023 8,541 2 View
I am running a protein ligand complex simulation using Gromacs 2021 on a Windows Subsystem for Linux. My laptop has Nvidia GeForce RTX 3050 GPU. When i run the simulation of Lysozyme tutorial (as...
07 March 2023 4,875 4 View
Using 1 MPI thread Using 8 OpenMP threads WARNING: Using the slow plain C kernels. This should not happen during routine usage on supported platforms. Back Off! I just backed up em.trr to...
28 February 2023 1,865 1 View
Hello colleagues! I found that my structure is not stable at the ground state, id. 0 Kelvin ( the crystal structure change before and after relaxation, but the energy is still negative) Thus I...
19 February 2023 8,379 7 View
Dear all Gromacs user, I am using Gromacs to run NVT and NVT equilibrium. Before the equilibrium, my input gro file shows all atoms (proteins, Zn, Na and Cl ions, and waters) stayed in the box...
18 February 2023 4,898 1 View
Hi every one. I want to read the results from my previous job but i have to create new part (selected DO NOT USE PARTS...) and cant import part. in defining initial state abaqus gives this...
11 February 2023 2,342 0 View
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 1,202 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 9,642 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 9,211 3 View
I'm doing the simulation in single method as always. I haven't changed any parameters.
20 January 2023 4,207 0 View
I have done homology modeling using i-tasser. I have successfully done docking for one of protein but after that it is showing error and empty files for rest of them. Same problem with ClusPro.
20 January 2023 8,647 1 View
In order to investigate the process of entering a protein into a cavity of a MOF, I used SMD, In the direction of the z-axis, the protein has entered the cell and exited from the other side. I...
20 January 2023 3,736 2 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 7,458 3 View
After selecting the residues of the protein for flexible docking, when I click on "Choose Torsions In Currently Selected Residues", under the " Flexible Residues" tab, I get this error:...
29 December 2022 2,504 1 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 1,451 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 1,451 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 1,938 0 View
On what basis should the Ψ and φ values be selected
21 November 2022 1,098 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 8,685 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 588 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 10,004 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 8,352 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 3,545 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 3,972 0 View