Hi, You can easily generate position restraints files yourself - have a look at one and learn about the column format from chapter 5. There is also gmx genrestr to help with this - but read the documentation first.
Mark On Tue, May 19, 2015 at 2:10 PM soumadwip ghosh <[email protected]> wrote: > Hi all, > I have some general doubts about the use of an itp file built by > some software. I am studying the dynamics of a DNA in presence of a > graphene sheet. I am using now the CHARMM27 force field and have obtained a > graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon > atoms and the terminal hydrogen atoms of the graphene sheet have been taken > into account according to the standard CHARMM directory. Now, do I need to > modify my aminoacids.rtp file in order to account for the atoms in the PDB > file? I have not done any pdb2gmx so do I really need to do that step? The > atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms > which describe the graphene framework in addition to other non-bonded > parameters. The equilibration steps are running without any hitches but I > am not getting whether the proper interaction (atomistic) would arise > between graphene and DNA atoms. As suggested by Justin i've switched over > to CHARMM27 force field and am looking at atlest 200 ns of production run. > Another question is, since I have not performed pdb2gmx on graphene, I dont > have a posre_graphene file. Is it gonna create some problem later during > mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre > file for graphene by some other method without doing pdb2gmx if this file > is mandatory? > > Hope I'm not asking for much. > > Regards, > Soumadwip > Research Fellow > IIT Bombay > 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 [email protected]. > -- 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 [email protected].
