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

[Md. Imrul Reza Shishir]

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.

Best regards

Md Imrul Reza Shishir


On Tue, Jun 7, 2016 at 10:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea