If I am not mistaken, and there is a chance that I am the length and force constant are used with grompp in ffbonded.itp in the force field directory. After the question mark everything else is indeed not read so it is mostly used by the users for clarification. But I believe that in the part that you posted it is used in case you want to add some optional parameters you remove the mark. Hopefully I am right, but please if it is not much do double check my comments.
________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Wednesday, June 3, 2015 8:58 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Questions about the topology file format On 6/3/15 1:55 PM, Ebert Maximilian wrote: > Hi there, > > I have two quick questions about the topology file format which I couldn’t > find in the documentary. The semi-colon is giving me some headache. Is it > always a comment which is written after? > > First: > > [ atoms ] > ; nr type resi res atom cgnr charge mass ; qtot > bond_type > 1 opls_135 1 IPA C1 1 -0.111600 12.01100 ; qtot > -0.112 CT > > is qtot and CT used for anything and is it interpreted since it is after the ; > Everything after ; is ignored. > Second: > > [ bonds ] > ; ai aj funct r k > 1 2 1 ; 1.5350e-01 2.5363e+05 ; C1 - C2 CT - CT > > are the values for r and k here used since they are after the ; and what is > C1-C2 and CT-CT used for and why another ;? > Not used for anything. Whatever software you used to produce the topology annotated it for whatever reason that the programmer decided was useful and in whatever manner he/she liked. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
