Hi, Ok, I didn't understand you because I didn't have enough information yet. IIRC your topology will still have to specify the constraint bond length, you can't have grompp infer it from the starting coordinates. You should also get a single molecule working correctly, because the symptoms of broken topology and broken initial coordinates are often not distinguishable. Prove the topology first when there cannot be an inter-molecular clash.
Mark On Mon, 7 Aug 2017 22:00 Maghesree Chakraborty <maghesre...@gmail.com> wrote: > Thank you for your response. I did not have tabulated potentials for bonded > interactions. I had tabulated potentials only for non-bonded > interactions. I had set constraints to be all-angles in my mdp file. I will > try using "constraint" interaction explicitly in my topology instead of > converting bonds and angles into constraints via mdp directive. > > On Mon, Aug 7, 2017 at 1:58 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Tabulated bonded interactions are the opposite of constraints. You can > > explicitly use a "constraint" interaction type in your topology, which > > sounds like a good start. See chapter five of the reference manual. > > > > Mark > > > > On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty <maghesre...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to run a CG simulation with only non-bonded interactions. I > > > have obtained the tabulated potentials for those interactions by > > > force-matching using VOTCA. I want all my bonds and angles to be > > > constrained as they are in the initial cg_conf.gro file. Since I do not > > > have tabulated potentials for bonded interactions, gromacs gives error > > if I > > > do not provide the bond and angle parameters (b0,kb and θ0 , kθ) in the > > > topology file. Then I tried setting the bond parameter (b0) to be the > > mean > > > of bond-length distribution in cg_conf.gro and the angle parameter (θ0) > > to > > > be the mean of the angle distribution in cg_conf.gro, I constrain the > > bonds > > > and angles with LINCS in my grompp file. During simulation, I get a lot > > of > > > LINCS warning and simulation is aborted. I am wondering if there is a > way > > > of constraining the initial configurations of the molecules as they are > > in > > > cg_conf.gro file in the absence of tabulated bonded potentials and not > > > forcing the molecules to have the bond-lengths and angles as specified > > by > > > the topology parameters. > > > > > > Thank you. > > > > > > Regards, > > > M. Chakraborty > > > -- > > > 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. -- 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.