[gmx-users] Maximum protein size for REMD?

[Mark Abraham]

Maybe. Either the model in the server is inapplicable for your system, or
you've input data for the model incorrectly.

Mark


On Thu, Apr 11, 2013 at 11:34 AM, Nikunj Maheshwari <
nixcrazyforher at gmail.com> wrote:

> I understand the point now. Bigger the system, closer will be the spacing.
> One thing though: The average energy (mu) returned by the web server for
> each temperature is 7-8 times more than the actual energy returned after
> REMD was over.
> Is there something we are missing here?
>
> Thanks.
>
> On Tue, Apr 9, 2013 at 6:42 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari
> > <nixcrazyforher at gmail.com> wrote:
> > > 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?
> >
> > You can space them however you want, but you will only get exchanges
> > if they are close enough in temperature. The spacing returned by the
> > generator is not small because it wants you to use excess compute
> > resources! It needs to be small for big systems.
> >
> > Mark
> >
> > > 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.
> > >> >>> --
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