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. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
