[gmx-users] Exclusions section in topology.

Siva Dasetty sdasett at g.clemson.edu
Tue Oct 6 16:13:21 CEST 2015

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

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

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