[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

Re: [gmx-users] In-Vacuo ligand only equilibration

On 4/13/15 12:38 AM, Iris Nira Smith wrote: 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 minimiza

Re: [gmx-users] In-Vacuo ligand only equilibration (Iris Nira Smith)

Thank you Justin for your insight to your previous response. I made adjustments to my equilibration .mdp file (below) to run as NVT in vacuo. Can you review and advise on corrections? eqb-nvt-invacuo.mdp ;Title = equilibration nvt (invacuo) ; define = -DFLEXIBLE ; ;Run parameters integrator =

Re: [gmx-users] In-Vacuo ligand only equilibration (Iris Nira Smith)

On 4/13/15 10:38 AM, Iris Nira Smith wrote: Thank you Justin for your insight to your previous response. I made adjustments to my equilibration .mdp file (below) to run as NVT in vacuo. Can you review and advise on corrections? Looks fine (don't use -DFLEXIBLE for MD in general, but it only