[gmx-users] problem in applying position restrain on protein

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 28 13:27:30 CEST 2009

nitu sharma wrote:
> Dear all,
> I am encountering problem in applying position restrain on my protein 
> which is with lipid bilayer . Actually I want to do simulation of system 
> protein-lipid bilayer to pack lipid around the protein for this  I want 
> to keep my protein constant and lipid should move around this .I am 
> doing this by applying strong position restrain on protein  with force 
> constant 100000.
> But the restrain not working on protein.

Probably due to the excessively large force that you posted as your result of 
energy minimization.  Position restraints don't guarantee that everything stays 
exactly where it is, they just provide an energy penalty for moving those atoms.

Have you done what has been asked of you and inspected the location of the large 
force?  You have to demonstrate that you're using initiative to solve your own 
problem.  I know I've seen at least one post, if not two, that have told you to 
look at your structure file and deduce the location of the large force.  That is 
usually the information necessary to solve this problem.


> I have included these lines in my topol_A.itp file and topol_B.itp file-
> ; Include position restrain file
> #ifdef POSRES
> #include "posre_A.itp"
> #endif
>  I have also included-
> define              =  -DPOSRES in em.mdp file.
> also edited posre.itp file with force constant 100000.
> Even after doing these things the restrain not working on protein thats 
> why my protein structure being disturbed .
> Can any one help me in solving this problem.
> Thanks a lot in advance.
> Nitu sharma
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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