Hi, In the group scheme you can turn on energy-group exclusions to get this working, but of course all of those states are sampling unphysical things from a broken forcefield. That can be OK, but you will have to be able to defend that claim.
Mark On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.a...@gmail.com> wrote: > Hello, > > I am running simulations of two protein domains in tip4p water and 0.15M > salt concentration that contain up to 650,000 atoms total. The protein > domains are separated from each other at the start of each simulation and I > am measuring how the distance between them changes over time. > > Now, I need to do the same simulations, but with electrostatics between > proteins and water turned off (with water-water, protein-protein, > ion-water, ion-protein electrostatics remaining). Then I need to repeat > that, but additionally turning off electrostatics between the two domains. > Water-water, ion-water, ion-protein, intra-domain electrostatics should > remain on. > > What will be the best way to do this? > > I am using CHARMM27 force field and the following settings to run the > production simulations: > > integrator = md > dt = 0.002 > nsteps = 1000000 ; 2ns > nstlog = 1000 > nstxout = 5000 > nstvout = 5000 > nstfout = 5000 > nstcalcenergy = 100 > nstenergy = 1000 > ; > cutoff-scheme = Verlet > nstlist = 20 > rlist = 1.2 > coulombtype = pme > rcoulomb = 1.2 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.2 > ; > tcoupl = Nose-Hoover > tc_grps = Protein Non-Protein > tau_t = 1.0 1.0 > ref_t = 300.0 300.0 > ; > pcoupl = Parrinello-Rahman > pcoupltype = isotropic > tau_p = 5.0 > compressibility = 4.5e-5 > ref_p = 1.0 > ; > constraints = h-bonds > constraint_algorithm = LINCS > continuation = yes > ; > nstcomm = 100 > comm_mode = linear > comm_grps = Protein Non-Protein > ; > refcoord_scaling = com > > > I have tried to use the energy groups (energygrp-table) to specify > interaction tables between water and protein, where I would set the > electrostatic potential to zero. However, given that energygrp-table and > Varlet cutoff-scheme are incompatible, I could not make it work. But it is > possible that I did something wrong. > > Thank you in advance, > > Aram > -- > 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.