[gmx-users] Position restrain of of different chain in fibril structure

[Justin Lemkul]

On 6/6/16 11:32 PM, Md. Imrul Reza Shishir wrote:
> Dear all
> good day.
>
> https://drive.google.com/open?id=0B9FUC_dv9IRoTUdHZENEN1FaOHc
>
> In the google drive file i attached all the file with forcefield file. I
> only deleted the nvt.trr file. As this file size very big.
>
> In this run i only use 7 chain of cellulose. to small the calculation step.
>
> Still after the energy minimization. When i run the nvt.mdp then the fibril
> structure broken. All chain aligned one by one.
>

Sorry, I see no reason for this.  Very strange.  Watch the trajectory from NVT 
and see if you can spot any weird behavior.  But there's nothing I can tell from 
this, and the files are so large that they keep crashing my VMD.  So it may help 
to simplify - make sure you can run a simulation with one chain, then two, etc. 
and see if you can identify what's going on.

-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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