[gmx-users] NVT equilibration in vacuum

[Justin Lemkul]

On 3/26/19 5:43 PM, Neena Susan Eappen wrote:
> Hello gromacs users,
>
> I am using gromacs to simulate a peptide in vacuum. I was wondering for the NVT equilibration step, are there any particular parameters to be changed for vacuum conditions as there is no position restraining on solvent molecules?

Preparing a vacuum system is not like a condensed-phase system. To do a 
simulation in vacuum, turn off PBC and set all cutoffs to zero (rlist, 
rvdw, rcoulomb).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================