Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation
Hello, Thanks for your reply. Regards, M. Chakraborty On Mon, Aug 7, 2017 at 4:56 PM, Mark Abrahamwrote: > 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 > 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 > > 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 > > > 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. > -- 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.
Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation
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 Abrahamwrote: > 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 > 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.
Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation
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 Chakrabortywrote: > 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.