Re: [gmx-users] hole in the simulation box

thank you for your suggestion, I've tuned the gmx solvate -radius parameter until I achieved the stability of the box dimensions in the NPT ensemble, now it seem the everything is working... thanks again, regards, Emiliano On 2017-08-01 00:10, Dallas Warren wrote: There are insufficient

Re: [gmx-users] hole in the simulation box

There are insufficient waters in the box to fill it up completely. Two solutions that come to mind, add more water so it reaches the appropriate simulated density under those conditions, or run under NPT until reaches appropriate simulated density then swap back to NVT. Catch ya, Dr. Dallas

[gmx-users] hole in the simulation box

Hi gromacs users, I am trying to simulate a crystal supershell (5x5x5 unit cells) with martini ff in gromacs 5. I build the system in aa representation, then I converted it in CG using the martinize.py script, following the tutorial, I've done a brief equilibration in water, the after the