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

[Md. Imrul Reza Shishir]

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.

-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*