From: Parag Adhangale (parag_adhangale_at_yahoo.com)
Date: Thu May 05 2005 - 16:23:52 CDT
Hi All,
I am trying to simulate a coarse grained water
model based on the GROMACS force field. NAMD crashes
and the last few lines in the output file are:
Info: Using GROMACS format force field!
Info: GROMACS TOPO FILE ff_v1_4_wat.itp
Info: GROMACS COOR FILE watercg_box.pdb
Info: SUMMARY OF PARAMETERS:
Info: 0 BONDS
Info: 0 ANGLES
Info: 0 DIHEDRAL
Info: 0 IMPROPER
Info: 0 VDW
Info: 1 VDW_PAIRS
ERROR: src/NamdState.C(158): Number of pdb and psf
atoms are not the same!
Info: Entering startup phase 0 with 6592 kB of memory
in use.
Info: Entering startup phase 1 with 6592 kB of memory
in use.
Info: Entering startup phase 2 with 6592 kB of memory
in use.
Info: Entering startup phase 3 with 6592 kB of memory
in use.
Info: PATCH GRID IS 7 (PERIODIC) BY 7 (PERIODIC) BY 7
(PERIODIC)
Info: REMOVING COM VELOCITY nan0x7fffffff
nan0x7fffffff nan0x7fffffff
Info: LARGEST PATCH (1) HAS 64 ATOMS
FATAL ERROR: Incorrect atom count in
WorkDistrib::assignNodeToPatch
----------------------------------------------
The GROMACS topology file reads:
: FORCEFIELD V1.4
[ defaults ]
1 1 no
[ atomtypes ]
;name mass charge ptype c6
c12
; polar type
P 72.0 0.000 A 0.0 0.0
[ nonbond_params ]
; i j funda c6 c12
P P 1 0.21558E-00 0.23238E-02
; attractive
;;;;;; 4 WATER MOLECULES
[ moleculetype ]
; molname nrexcl
W 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P 1 W W 1 0
Any help would be greatly appreciated.
Thanks
Parag
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