[gmx-users] NVT equilibration in vacuum

Erik Marklund erik.marklund at kemi.uu.se
Wed Mar 27 12:56:26 CET 2019

Additionally, be aware of the tumbling ice cube effect and set comm-mode to angular to avoid it.

Kind regards,
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 27 Mar 2019, at 00:53, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

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 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<mailto:jalemkul at vt.edu> | (540) 231-3129


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