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

[Justin A. Lemkul]

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.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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