[gmx-users] changing charged groups in CHARMM RNA

[maria goranovic]

This must be specific to charmm's implementation in gromacs? Out of
curiosity, why can one not use charge groups ?

On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> maria goranovic wrote:
>
>> Dear List
>>
>> I was looking at the charged groups in a charmm nucleotide, and could see
>> several groups containing 4 to 14 atoms with integer charges. However, the
>> default topology does not have these charged groups. each atom is given a
>> charged group in the default topology. Can we foresee any problems in
>> replacing the default charged groups generated by pdb2gmx by custom-made
>> charged groups of integer values ? Along the same lines, will this lead to a
>> significant increase in performance, besides the advantage of
>> transferability ?
>>
>
> With the CHARMM force field, you should not use charge groups.  Each atom
> should be its own "group."
>
> -Justin
>
>
>  Thanking you in advance
>>
>> Maria
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> ========================================
>
> 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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