[gmx-users] Position restrain of 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.

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.

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.

​Thank you very much.​

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