[gmx-users] Using make_ndx to couple molecules before pulling simulation

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Oct 27 22:27:39 CET 2014

Dear Users

In my .gro file the molecules section contains the following :-
[ molecules ]
; Compound        #mols
DNA_chain_D         1
Protein_chain_L     1
Protein_chain_H     1

Now , I want to do a pulling simulation where , I want both chain L and
chain H to be pulled simultaneously as an unit while keeping the chain D
I am planning to position restrain chain D by specifying a #ifdef POSRES_D
block in the topology for chain D.
In my pull code , I want to specify pull_group0 = Chain_D and pull_group1 =
Chain_P , where Chain_P = total of Protein_chain_L and Protein_chain_H.
Following Dr. Lemkul's tutorial on Umbrella Sampling , I understand that I
can use make_ndx to achieve the same.

My DNA part consists 488 atoms and Protein part consists 4527 atoms. While
using make_ndx I tallied the number of atoms from the command prompt with
the residue numbers in my .gro ( structure / coordinate ) file and named
the DNA chain as Chain_D and the two protein chains as Chain_P.

I believe that this is the correct approach before I run the pulling

I request the experienced users to suggest and comment on my understanding.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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