Hi Mark, I am not sure I understood. If I for example say "energygrp-excl = Protein Water" would not I turn off all the non-bonded interactions between water and protein? Or did you mean something else?
Thanks, Aram > 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.