Hi, Sometimes. It depends exactly which functions and function types, and whether it's part of a moleculetype. If you don't want something, don't include it :-)
Mark On Thu, 22 Dec 2016 10:07 Mohsen Ramezanpour <ramezanpour.moh...@gmail.com> wrote: > Dear Gromacs users, > > I have a new file with both bonded and nonbonded parameters for some atom > types in it. I want to use these new parameters for simulation and ignore > the parameters in force field ( if there is any parameter already exist). > > 1) If I add the lines from each section of new file at the end of > corresponding section at ffbonded.itp and ffnonbonded.itp files, do I still > need to comment out all the present parameters or they will be all > overwritten by new defined parameters? > > 2) How if I just #include new file after inclusion of normal force field? > Will it overwrite previous parameters? > > Reading gromacs forum discussions and manual, I still was not sure of that > (I am using gromacs versions 4 and 5). > > > *From manual 5.8.3.* > *Adding atom types* > > As of GROMACS version 3.1.3, atom types can be added in an extra [ > atomtypes ] section > after the the inclusion of the normal force field. After the definition of > the *new atom type(s)*, ad- > ditional non-bonded and pair parameters can be defined. In pre-3.1.3 > versions of GROMACS, the > new atom types needed to be added in the [ atomtypes ] section of the force > field files, be- > cause all non-bonded parameters above the last [ atomtypes ] section would > be overwritten > using the standard combination rules. > > > Best, > Mohsen > > > > -- > *Rewards work better than punishment ...* > -- > 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. > -- 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.