On 1/09/2011 10:34 AM, Dr. Vitaly V. Chaban wrote:
On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul<jalem...@vt.edu> wrote:
Dr. Vitaly V. Chaban wrote:
Hi, ALL
I have a question about the charge defined in the topology file.
It seems to me that the charge for each atom apprears twice in
different sections of the topology files.
------------------------------------------------------------------------------
One is
[ atomtypes ]
;name mass charge ptype c6 c12
The other is
[ atoms ]
; id at type res nr residu name at name cg nr charge
------------------------------------------------------------------------------
And the charge number in [ atomtypes ] are always 0.0.
Which one is actually read by gromacs program ?
That one which is mentioned the last
That is true in the case where grompp finds multiply defined types for
bonded interactions and atom types; the charges in ffnonbonded.itp are never
used by any program. The reason for their existence is not clear, but
perhaps they were used by older versions or were intended for some
streamlined force field organization that never came to fruition.
I believe, this column is intended for aminoacids for which there
should be a consistent set of parameters including charges. This is
what we have in AMBER.
However that only works if the charge is the same for that atom type in
each possible residue. That's not a very effective constraint.
Mark
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