Dear all, As the Verlet cut-off scheme does not support energygrp-excl parameter yet, we are looking for an alternative to exclude all non bonded interactions between the frozen atoms.
The gromacs manual (section 5.4) states that all the non bonded interactions between the pairs in the [ exclusions ] section of the topology file will be excluded. In order to test this we have considered a small system comprising 13 charged atoms (oplsAA-ff) and ran a NVE simulation where all the atoms are frozen. We did the simulation with and without including the [ exclusions ] section in the topology file. We found that all the LJ -SR interactions are indeed 0 but the Coulomb-SR interactions are not exactly zero. Note that we are not using PME for the coulomb type and there is no solvent. In order to understand the contribution of each atom to the Coulomb-SR we have created energy groups of some of the atoms and ran the simulations using only CPUs (-nb cpu). Below are the average energies obtained using g_energy tool with and without exclusions. Energy Average ( with exclusions ) Average (without exclusions) ------------------------------------------LJ (SR) 0863710Coulomb (SR) -7.63E-06-619.943Coul-SR:O1-O1 -10.6078-10.6078LJ-SR:O1-O1 00Coul-SR:O1-O2 -36.58106.48LJ-SR:O1-O2 011.4136Coul-SR:O1-H1 7.51731-22.0658LJ-SR:O1-H1 072.0831Coul-SR:O1-rest 50.2783-191.784 LJ-SR:O1-rest 035631.6Coul-SR:O2-O2 -31.5359-31.5359LJ-SR:O2-O2 0 0Coul-SR:O2-H1 12.9614-45.7467LJ-SR:O2-H1 03023.75Coul-SR:O2-rest 86.6905-555.719LJ-SR:O2-rest 043085.1Coul-SR:H1-H1 -1.331810.0595622 LJ-SR:H1-H1 0-0.00987022Coul-SR:H1-rest -17.815245.9682 LJ-SR:H1-rest 0281888Coul-SR:rest-rest-59.57785.0095LJ-SR:rest-rest 0 499998 Why is there a contribution of Coul-SR energies from some of the pairs? Also, there is only one O1 atom in the system. So what does Coul-SR O1:O1 mean? We have also included the corresponding pair [O1 O1] in the exclusions section. Below is a copy of the mdp file used. dt = 0.002 nsteps = 500000 nstcomm = 100 comm-grps = System nstlist = 10 ns_type = grid nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 2500 nstenergy = 2500 nstxout-compressed = 2500 compressed-x-grps = System cutoff-scheme = Verlet verlet-buffer-tolerance = -1 pbc = xyz rlist = 1.0 coulombtype = Cut-off rcoulomb = 1.0 rvdw = 1.0 vdwtype = Cut-off constraints = h-bonds constraint_algorithm= lincs freezegrps = GRO freezedim = Y Y Y energygrps = O1 O2 H1 Thanks in advance for your help, -- Siva Dasetty -- 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.
