[gmx-users] steady

[Justin A. Lemkul]

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
> 

-- 
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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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