[gmx-users] NVT problem

[Justin Lemkul]

On 3/15/14, 6:31 PM, Andres Ortega Guerrero wrote:
> Thanks Justin for all your Help, i´m going to do all you suggesta and prepare a new structure,
> but before that i would like to try with a POSRE for the protein 10000 due to i am using 1000,
> also i would like to tell you, that due to the channel , is too big, in order to embebed in a 512 POPC Box,
>   i deleted some residues located at the terminal (inside the membrane) , so i think this could be
> one reasson of the problem.
>

That sounds like a rather serious perturbation, but not one that would cause a 
crash like this; more so that it may cause artifacts in your dynamics.

I suspect that a stronger restraint force constant will not have any effect; one 
should not have to apply such a level of bias just to force something into 
running, especially if proper energy minimization was done (which I am still not 
convinced is the case, for reasons stated previously).

-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 601
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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