[gmx-users] Maximum protein size for REMD?

[Nikunj Maheshwari]

Thats true with our case as well. The spacing was very small, and we got
almost 70 replicas for our protein between 280-410K.
That's why, we are thinking of any alternate way of getting the spacing,
and started using polynomial fit of the average energies we obtained from
our first run. Do you have any thoughts on that?

On Tue, Apr 9, 2013 at 2:03 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> I used the REMD temperature generator. Needless to say, we got really
> tight spacing and the enhancement to the sampling was probably small. The
> whole setup was pretty experimental. The run was completed.
>
> Erik
>
> On 9 Apr 2013, at 10:01, Nikunj Maheshwari <nixcrazyforher at gmail.com>
> wrote:
>
> > How did you get the final temperature spacing for the run? Did you get
> the
> > fitted values using polynomial fit?
> > Was the run completed?
> >
> > On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> wrote:
> >
> >> I've tried one with 666 aa, but with no publishable results.
> >>
> >> On 9 Apr 2013, at 09:47, Nikunj Maheshwari <nixcrazyforher at gmail.com>
> >> wrote:
> >>
> >>> Dear all...
> >>>
> >>> Does anyone has any idea what is the maximum protein size for which a
> >>> successful REMD run has taken place?
> >>> We have went through lots of research papers, but could not find any
> >>> protein/peptide above 100 aa related to REMD.
> >>> We have a protein of 292 aa.
> >>>
> >>> Thanks.
> >>> --
> >>> 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
>
> --
> 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
>