[gmx-users] cgnr

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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