[gmx-users] Simple gas-phase minimization help

[Justin Lemkul]

On 6/14/16 1:02 PM, Tarick E wrote:
> Hey everyone,
>
> I am new to this, so please forgive me if this has been asked before.
>
> I am trying to conduct an energy minimization in vacuum on individual
> proteins and small peptides at a constant temperature, but I am having

There is no temperature during energy minimization.

> trouble with this. Is there any documentation someone can lead me to for
> producing a vacuum-phase minimization .mdp file? I have been trying to edit
> the various .mdp files provided in the Lysozyme tutorial written by Justin
> Lemkul, but I haven't had any luck and I can't seem to locate any info in
> the Gromacs users manual.
>

Set all cutoffs to zero and do not use PBC.  Then you're in vacuum.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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