[gmx-users] simulate Gas Phase system

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 4 12:46:30 CEST 2008

Nuno Azoia wrote:
> Chih-Ying Lin wrote:
>> Hi
>> to simulate the gas phase system, before running MD on the gas phase 
>> system
>> I have to use the "editconf" command.
>> But, I DO NOT  use "genbox" command.
> I'm new to Gromacs, but I think that if you do that you will running 
> simulation in vacuo. Maybe it a good approximation to gas phase, but 
> if your box is empty it will be a vacuo simulation.

Technically yes, but gases are mostly empty space anyway.  I have seen 
examples of gas phase simulations where the molecules were separated by 
50 nm in the simulation box (Oostenbrink, et al. (2004) J. Comp. Chem. 
25: 1656-1676.


>> Right??
>> thanks
>> Lin
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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