[gmx-users] changing charged groups in CHARMM RNA

[maria goranovic]

thank you for the reply. That settles that.

On Tue, Mar 22, 2011 at 2:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> maria goranovic wrote:
>
>> This must be specific to charmm's implementation in gromacs? Out of
>> curiosity, why can one not use charge groups ?
>>
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html
>
> -Justin
>
>
>> On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>> --
>> 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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