[gmx-users] REMD temperature spacing formula

[Mark Abraham]

On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari <nixcrazyforher at gmail.com
> wrote:

> Thanks for that link.
> I have used it, but it only takes system size properties. It doesn't take
> the potential energy values at all.
>

Actually it does, inasmuch as it uses parameters fitted to observed energy
values, which you'd know from reading the abstract of the cited paper ;-).


> I am looking if someone has used any alternate for temperature spacing
> generation?
>

Not sure what you're asking for. But you could try the REMD how-to guide in
<shameless plug>http://pubs.acs.org/doi/abs/10.1021/ct800016r</shameless
plug>, or the works of DA Kofke or UHE Hansmann will likely be instructive.

Mark

On Thu, Apr 4, 2013 at 1:16 PM, rama david <ramadavidgroup at gmail.com> wrote:
>
> > Dear
> >
> > http://folding.bmc.uu.se/remd/ this may help you.
> >
> >
> > With best regards
> >
> >
> > On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari <
> > nixcrazyforher at gmail.com
> > > wrote:
> >
> > > Dear all,
> > >
> > > We are stuck at the last stage of running a successful REMD.
> > > We have obtained average potential energy by fitting the energy values
> > from
> > > initial MD.
> > > We want to get the temperature spacing for 72 replicas, starting from
> > 280K.
> > > We have gone through numerous papers, but none of them explain clearly
> > how
> > > they got the spacing values.
> > > Is there any equation/formula/web utility which gives the spacing?
> > >
> > > Any help will be highly appreciated.
> > >
> > > Thank you.
> > > Nikunj & Suhani
> > > --
> > > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>