Re: [gmx-users] changing charged groups in CHARMM RNA

Justin A. Lemkul Tue, 22 Mar 2011 06:57:11 -0700


maria goranovic wrote:

This must be specific to charmm's implementation in gromacs? Out ofcuriosity, 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 <jalem...@vt.edu<mailto:jalem...@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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Re: [gmx-users] changing charged groups in CHARMM RNA

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