Re: [gmx-users] NVT equilibration in vacuum

[Erik Marklund]

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

Kind regards,
Erik
__
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.markl...@kemi.uu.se

On 27 Mar 2019, at 00:53, Justin Lemkul 
mailto:jalem...@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

--
==

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

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

==

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Re: [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

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

==

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[gmx-users] NVT equilibration in vacuum

[Neena Susan Eappen]

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?

Thank you,
Neena
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