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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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