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

Justin Lemkul jalemkul at vt.edu
Tue Oct 28 02:34:22 CET 2014

On 10/27/14 5:27 PM, Agnivo Gosai wrote:
> 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
> fixed.
> 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
> simulation.
> I request the experienced users to suggest and comment on my understanding.

Use gmxcheck to verify the contents of the index group and you can decide for 
yourself if it's correct.  In reality, though, you don't even need make_ndx 
here.  You have a DNA as the reference and Protein as the pulled group.  Both 
are default groups, so

pull_group0 = DNA
pull_group1 = Protein

does what you want with no extra effort.  You can of course combine that with 
the restraints via define statement if you need to.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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