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

[Justin Lemkul]

On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote:
> Dear all
> I have a structure file of cellulose nano fibril of 36 chain (each have 40
> residue). I want to simulate it as a single compound. I try to run the
> simulation with OPLS-AA force field. After energy minimization when i run
> the equilibrium step then the fibril structure broken and all the chain
> aligned in a single chain like structure. I want to restrain the position
> of chain in there original sheet like structure. But I am  not able to
> define.
>
> In the dropbox i attached my simulation structure image file. Initially, it
> was 7 sheet of 36 cellulose chain (each chain 40 residues). I check the
> structure (gro file) every stage in VMD after new box creation, solvating,
> energy minimization. The initial structure is not broken. But after
> equilibrium stage when I run nvt.mpd it will break it initial stage. And
> all 36 chain aligned like output structure.
>
> *gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce -missing*
>
> *gmx_mpi editconf -f test_fibril_processed.gro -o
> test_fibril_newbox.gro -c -d 1.0 -bt cubic *(This box set-up command)
>
> I also attached nvt.mdp, npt.mdp and md.mdp file. This simulation is
> trial run for long time simulation. How should i restrain the position
> of my structure.
>
>
> In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input
> and output structure image in vmd.
>
> https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0
>
> Thank you very much.
>

Please upload the actual coordinate files and any relevant topologies.  I don't 
see how setting up that structure in a cubic box would lead to such a structure.

-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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