Marcelo A. Carignano wrote:
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:
check the 14 energy.
---------
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
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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