[gmx-users] exclusions

[Steven Neumann]

I guess I need to write [ exclusions ] as TUB is composed of other
energygrps. I have 2516 atoms, that would be difficult to write [
exclusions ] manually, would you recommend any script? I am not programming
:(

Steven


On Thu, Dec 5, 2013 at 3:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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