[gmx-users] position restrained minimization on the one part of a system

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 26 15:42:44 CEST 2011

Atila Petrosian wrote:
>  I want to use define  = -DPOSRES_Protein_chain_A for step 1.
>  is it true?

Not per the topology you posted earlier.  Your only option (at this point) for 
restraining the protein is -DPOSRES, which restrains all the chains.

If you want to restrain parts of your structure, you will likely need to create 
custom posre.itp files for the different chains (or whatever merged combinations 
of them) using genrestr and perhaps custom index groups generated by make_ndx.

A trivial example of such a procedure is described in the protein-ligand 
tutorial I wrote:




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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