Thanks for your quick reply, so it a fact that I can bypass the missing bonds force constant field in grompp by using these constraints?
________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Thursday, June 11, 2015 12:37 PM To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] problem using grompp Hi, SETTLE is a constraint algorithm for water. LINCS and SHAKE are the available general-purpose constraint implementations - see the manual section headed "constraint algorithms". Mark On Thu, Jun 11, 2015 at 10:39 AM Sotirios Dionysios I. Papadatos < si.papada...@edu.cut.ac.cy> wrote: > Dear community, > > > I am trying to set parameters for a molecule that doesn't exist in gromacs > "library". > > I have found all the required data from the literature, apart from bond > force constant (Kb). > > There seems to be a way to overcome this but using constraints on all the > bonds using the Settle algorithm. My problem is that even by looking > through the manual I haven't found a way to implement it. I believe I do > know that it has to be used in the .mdp file but I don't know how. > > So far I have tried adding these two lines in the .mdp file: > > constraints=all-bonds > > constraint-algorithm=settle > > But it doesn't seem to do the trick, it still prints out the same error! > -- > 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. -- 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.