Hi, Below is my .mdp code for pulling as found in the tutorial by Justin Lemkul. I made the required changes to match my version syntax.
pull = umbrella pull_ngroups = 2 pull_group0 = Protein_chain_A pull_group1 = DNA_chain_B pull_group2 = DNA_chain_C pull_geometry = distance ; simple distance increase pull_dim = Y N N pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_rate2 = 0.01 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_k2 = 1000 pull_start = yes ; define initial COM distance > 0 When I tried to grompp using this code, it generates an error: Fatal error: Group topol_Protein_chain_A referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. I searched for the solutions in the Gromacs forum and found it might be due to name mismatch. But, in my case, the names are exactly same as referenced in the *.mdp file. Below is the molecule names from the topol.top file. [ molecules ] ; Compound #mols Protein_chain_A 1 DNA_chain_B 1 DNA_chain_C 1 SOL 33542 NA 125 CL 98 Can you please help to solve the problem? I tried with changing the names to Protein and DNA (the residue types) and changing the ngroups to 3. Nothing worked. Regards, Souparno Adhikary University of Calcutta, India. -- 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.
