[gmx-users] Position restrain of structure

[Md. Imrul Reza Shishir]

Dear Justin
Thank you for your reply.
This is my simulation structure 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.

Best regards

Md Imrul Reza Shishir


On Fri, Jun 3, 2016 at 6:45 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/1/16 11:22 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
>>
>
> If you can upload before and after images (to some file sharing service,
> and provide us a URL on the list) of what's going on, it would help.  This
> could either be an issue with (1) PBC, (2) setting up the box incorrectly,
> (3) incorrect topology, or (4) some combination of all of the above.
>
> of chain in there original sheet like structure. But I am  not able to
>> define.
>>
>> I start with this pdb2gmx command .
>>
>> gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce
>> -missing -merge all
>>
>> How can i define *chainsep* option in the pdb2gmx command.
>>
>> ------------------
>> ATOM    842  OB  UN1    40      29.218  50.526  48.874  1.00  0.00
>> ATOM    843  HOB UN1    40      28.409  50.951  48.646  1.00  0.00
>>
>> ATOM    844  HOA UN1    41      15.236  41.916 250.988  1.00  0.00
>> ATOM    845  OA  UN1    41      15.877  41.231 251.063  1.00  0.00
>> ------------------
>>
>> Residue 40 and 41 is the terminating and initial next of next chain.
>> How i can define id_or_ter for *chainsep* option.
>>
>>
> -chainsep creates distinct molecules based on TER delimiters or chain
> identifier characters.  See the PDB format documentation for more.
>
> In nvt, npt or md file i use
>>
>>
>> -----
>> define                  = -DPOSRES      ;
>> refcoord_scaling        = no            ;
>>
>> --------
>>
>> for position restrain this is the right way. Or I have to do something
>> else. Actually my main target to retrain the fibril structure and 36 chain
>> are formed 7 sheet not a single chain like structure.
>>
>>
> That should restrain the atoms, although the choice of refcoord_scaling
> may not be appropriate.  But two lines of an .mdp file is insufficient to
> judge whether or not you're doing things correctly.
>
> -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