[gmx-users] Maximum protein size for REMD?

[Nikunj Maheshwari]

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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