Dear all,
I have encountered an unexpected behavior in which nonbonding values for
close intermolecular pairs do not appear to be always present. I have
reduced this problem to the configurational energy of two triatomic
isomers. The LJ values correctly rise ten orders of magnitude upon
deletion of a common superfluous atom in each molecule (O). I'm using
version 3.3.1 and this problem is present in both single and double
precision versions. Below are the input files for the triatomic
system, as well as their corresponding energies as obtained by gmxdump.
grompp.mdp (used for both diatomic and triatomic systems)
title = TwoMolecules
integrator = md
dt = 0.001
nsteps = 1
pbc = xyz
rlist = 0.7
rvdw = 0.7
tcoupl = no
pcoupl = no
--
conf.gro (triatomic system)
Chol
6
1CHO O 1 0.742 1.670 2.176
1CHO C2 2 0.615 1.758 1.580
1CHO C3 3 0.861 1.928 0.597
2CHO O 4 0.450 2.133 0.163
2CHO C2 5 0.445 2.285 0.619
2CHO C3 6 0.637 1.761 1.528
5.000000 5.00200 5.00000
--
topol.top (triatomic system)
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 0.125 0.5
[ atomtypes ]
;name mass charge ptype sig eps
C2 14.0300 0.300 A 0.39057 0.49371
C3 15.0300 0.400 A 0.39057 0.73220
O 16.0000 -0.694 A 0.30647 0.71128
[ nonbond_params ]
; i j func sig eps
C2 C2 1 0.39057 0.493712000
C2 C3 1 0.39057 0.601240800
C2 O 1 0.34852 0.592579920
C3 C3 1 0.39057 0.732200000
C3 O 1 0.34852 0.721656320
O O 1 0.30647 0.711280000
[ moleculetype ]
ACHO 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 O 1 1CHO O 0 0.000 16.00
2 C2 1 1CHO C2 0 0.000 14.03
3 C3 1 1CHO C3 0 0.000 15.03
[ system ]
; name
Two molecules
[ molecules ]
; name number
ACHO 2
--
gmxdump -e ener.edr (for above triatomic system)
time: 0.00000e+00 step: 0
Component Energy Av. Energy Sum Energy
LJ (SR) -3.83649e-01 0.00000e+00 -3.83649e-01
Coulomb (SR) 0.00000e+00 0.00000e+00 0.00000e+00
Coulomb (LR) 0.00000e+00 0.00000e+00 0.00000e+00
Potential -3.83649e-01 0.00000e+00 -3.83649e-01
Kinetic En. 3.24877e-07 0.00000e+00 3.24877e-07
-----------------------------------------------------------------------------------------------------------
conf.gro (diatomic system)
Chol
4
1CHO C2 1 0.615 1.758 1.580
1CHO C3 2 0.861 1.928 0.597
2CHO C2 3 0.445 2.285 0.619
2CHO C3 4 0.637 1.761 1.528
5.000000 5.00200 5.00000
--
topol.top (diatomic system)
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 0.125 0.5
[ atomtypes ]
;name mass charge ptype sig eps
C2 14.0300 0.300 A 0.39057 0.49371
C3 15.0300 0.400 A 0.39057 0.73220
[ nonbond_params ]
; i j func sig eps
C2 C2 1 0.39057 0.493712000
C2 C3 1 0.39057 0.601240800
C3 C3 1 0.39057 0.732200000
[ moleculetype ]
ACHO 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 C2 1 1CHO C2 0 0.000 14.03
2 C3 1 1CHO C3 0 0.000 15.03
[ system ]
; name
Two molecules
[ molecules ]
; name number
ACHO 2
--
gmxdump -e ener.edr (for diatomic system)
time: 0.00000e+00 step: 0
Component Energy Av. Energy Sum Energy
LJ (SR) 2.83815e+10 0.00000e+00 2.83815e+10
Coulomb (SR) 0.00000e+00 0.00000e+00 0.00000e+00
Coulomb (LR) 0.00000e+00 0.00000e+00 0.00000e+00
Potential 2.83815e+10 0.00000e+00 2.83815e+10
Kinetic En. 1.25001e+18 0.00000e+00 1.25001e+18
Total Energy 1.25001e+18 0.00000e+00 1.25001e+18
--
Thank you,
Steve
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