[gmx-users] Re: which charge is used in gromacs program

[Dr. Vitaly V. Chaban]

On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul <jalemkul at 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.




-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA