Dear all, I want to minimize my system to relax the solvent with the positions of heavy atoms within the protein restrained. I searched the archives and got the idea that I need to put something like this in topology:
#ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif But I still have no idea how to get the heavy atoms restrained. Could anybody tell me how to do this? I want to use gromos54a7 ff to simulate my collagen. As Justin suggested, I need to study the original paper "Definition and testing of the GROMOS force-field versions 54A7 and 54B7" to write my .mdp file. In the paper it says, 1. Each system was energy minimised to relax the solvent with the positions of the heavy atoms within the protein and RNA restrained. 2. All solute atom positions were restrained to their positions in the initial structure through a harmonic potential energy term with force constant of 2.5 9 104 kJ mol-1 nm-2. Could anybody tell me how to restrain the heavy atoms of protein, and how to get the solute atom positions restrained with a harmonic potential energy term with a certain constant? I searched the archives, and got the idea that I need to define it in the topology like the water oxygen being defined. What should I do with my posre_protein_chain_A.itp and topol_protein_chain_A_itp files? #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif Thanks a lot in advance. -- 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.
