[gmx-users] steady

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 6 13:18:34 CEST 2008

shahrbanoo karbalaee wrote:
> hi justin
> in during making mix solvent (30%  for example) after making box  I
> use trjconv  -pbc .My pdb file lost the the arrange and it  need long
> time for equilbrate and steady density.Is it right? or any suggestion
> about it?

What option are you giving trjconv -pbc (whole, nojump, etc.)?  Why do you need 
this?  If your goal is to create a mixed solvent, simply using normal periodic 
boundary conditions during the simulation should be all you need. 
Post-processing will likely give you a distorted unit cell.


> thanks


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list