[gmx-users] Missing LJ interaction

[Steve Fiedler]

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