[gmx-users] changing charged groups in CHARMM RNA

[Justin A. Lemkul]

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

========================================