Re: [gmx-users] Implicit solvent simulation

Hi, The implicit solvation implementation was broken with multiple threads for quite a few years, I'm afraid. So we have removed it for the upcoming 2019 release. I strongly recommend running it with only one thread (so use -ntmpi 1), or use the version in GROMACS 4.5.7 if you need the performance

[gmx-users] Implicit solvent simulation

Hello dear users! I'm trying to set up an implicit solvent simulation of a protein in gromacs, but I haven't found much about the details of how to do it. After generating topology: gmx pdb2gmx -f protein.pdb (I selected the amber99sb forcefield and none for water) I've done an energy minimiza

Re: [gmx-users] Implicit solvent simulation of protein folding

UPDATE: I found these parameters to work: http://comments.gmane.org/gmane.science.biology.gromacs.user/52770 Now I have a follow up question. It seems that at 300K my unfolded protein chain quickly collapses into some random conformation and more or less stays that way without much conformationa

[gmx-users] Implicit solvent simulation of protein folding

Hi everyone, I’m trying to run protein folding simulations with implicit solvent and the Amber99sb-ILDN forcefield. My problem is that I cannot get a stable simulation after energy minimization. Either mdrun stops after lots of LINCS warnings or the simulation finishes but the atom coordinate