[gmx-users] cgnr

[Marcelo A. Carignano]

Dear all:

I'm running a test case defining all the interaction parameters in the
topol.top file. My system consist of two NH3 molecules.
Every thing goes well except for the role played by the "cgnr" values:
Depending on how I assign these numbers the calculated Coulombic
interaction changes. If I put the four atoms in the same group, the
energy is not correct. If I put the four atoms in four different chnr's,
the Coulombic interactions are OK:

---------

Using (1234) cgnr: 

@ s0 legend "LJ-(SR)"
@ s1 legend "Coulomb-(SR)"
    0.000000   -0.004986    0.195137
    0.001000   -0.004989    0.194469

------------

@ s0 legend "LJ-(SR)"
Using (1111) cgnr:

@ s1 legend "Coulomb-(SR)"
    0.000000   -0.004986  145.684219
    0.001000   -0.004989  145.818558


Can anyone help me to understand this effect?
I'm using Version 3.3.1. 

Many thanks,
              Marcelo Carignano

--------------------

"topol.top":
;-------------------------------------------------------

[ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
  1		2		yes		1.0	1.0

[ atomtypes ]
;name  at.num      mass        charge   ptype    V		W
    N    7 	14.00670       -1.026      A   0.336	     0.87864
   HN    1 	 1.00800        0.342      A   0.	     0.

; define the NH3 model

[ moleculetype ]
; molname	nrexcl
NH3		2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge       mass
     1	    N	   1	NH3     N0      1      -1.026	   14.00670
     2	   HN	   1	NH3     H1      2       0.342	   1.00800
     3	   HN	   1	NH3     H2	3       0.342	   1.00800
     4	   HN	   1	NH3     H3	4       0.342	   1.00800

;[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge       mass
;     1	    N	   1	NH3     N0      1      -1.026	   14.00670
;     2	   HN	   1	NH3     H1      1       0.342	   1.00800
;     3	   HN	   1	NH3     H2	1       0.342	   1.00800
;     4	   HN	   1	NH3     H3	1       0.342	   1.00800

[ constraints ]
; i     j       funct   distance
1       2       1       0.10124       ; N - H1
1       3       1       0.10124       ; N - H2
1       4       1       0.10124       ; N - H3
2       3       1       0.162417      ; H1 - H2
2       4       1       0.162417      ; H1 - H3
3       4       1       0.162417      ; H1 - H3

[ system ]

[ molecules ]
NH3	  2


------------------------------------
conf.gro:

test
   8
    1NH3     N0    1   1.644   0.519   1.853
    1NH3     H1    2   1.729   0.548   1.808
    1NH3     H2    3   1.657   0.422   1.880
    1NH3     H3    4   1.637   0.572   1.939
    2NH3     N0    5   2.104   0.086   1.075
    2NH3     H1    6   2.115  -0.006   1.035
    2NH3     H2    7   2.071   0.072   1.170
    2NH3     H3    8   2.196   0.126   1.083
   20. 20. 20.


------------------------------------
grompp.mdp:

title                    = test
cpp                      = /usr/bin/cpp
include                  =
define                   =

integrator               = md
tinit                    = 0
dt                       = 0.001
nsteps                   = 1

nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 3.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = Cut-off
rcoulomb                 = 3.0
epsilon_r                = 1
vdw-type                 = Cut-off
rvdw                     = 3.0

Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = yes
gen_temp                 = 220.
gen_seed                 = 173529

constraints              = all-angles
constraint-algorithm     = shake