thank you for the reply. That settles that. On Tue, Mar 22, 2011 at 2:56 PM, Justin A. Lemkul <jalem...@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 <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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Maria G. Technical University of Denmark Copenhagen
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