[gmx-users] A simple question

Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the arom

[gmx-users] In-Vacuo ligand only equilibration

Hello, I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimization with the em-invaco.mdp file below (in abse

[gmx-users] Can NAMD simulation solve the problem of coordinate clash in a structural model?

Dear all, I modelled a structural model of a complex containing two large proteins. There are serious coordinate clashes between these two proteins in the model. Can I expect to do Gromacs simulation to solve the problem of cooridnate clash and obtain a more rational model? Best regards, Yepin

Re: [gmx-users] How to add a repulsive harmonic potential

Thank you for your help. Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these ligands. The reason why I add some ligand molecules(not one