[gmx-users] exclusions

[Justin Lemkul]

On 12/5/13 9:48 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> How can I apply exclusions of non-bonded parameters within my
> [moleculetype] - I the positions of this molecule is restrained so all
> non-bonded should be excluded. Would that need [ exclusions ] or
> energy-monitor group can be applied?

Either set nrexcl to a sufficiently large number that encompasses the longest 
possible bonded geometry or write an [exclusions] directive yourself.

> what shall i specify
> energy-monitor group = TUB TUB
>

Assuming you mean energygrp-excl = TUB TUB, that would also work.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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