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.
-Justin
thanks
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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