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.