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.
