[gmx-users] Study of sampling of villin headpiece

[Mark Abraham]

Hi,

OK, maybe dialanine is smaller than things you've already tested (though it
is surprisingly challenging, as you will see in the enhanced-sampling
literature). Perhaps you can estimate from your CG work how many
independent samples you need for a converged simulation as a function of
simulation degrees of freedom. Then your available compute resources can be
used to estimate an upper bound for the size of a test case.

Mark

On Mon, Aug 3, 2015 at 1:34 PM Mario Fernández Pendás <mariofp77 at gmail.com>
wrote:

> Hi Mark,
>
> Thank you very much for your answer.
> The main problem is that there is no previous literature because this is a
> new integration methodology that we are developing. I have tested my
> methods in a coarse-grained toy system and I was trying to do something
> similar in a more realistic system.
>
> Thank you very much for your suggestions.
>
> Best,
> Mario
>
> 2015-07-30 13:51 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > I do not think it is sensible to attempt to measure the relative
> efficiency
> > of two different methods in the absence of evidence that either has
> sampled
> > approximately ergodically. This is why many approaches to enhance
> sampling
> > start testing with toy systems like alanine dipeptide. You should check
> out
> > the literature for those methods you are comparing ;-)
> >
> > Mark
> >
> > On Thu, Jul 30, 2015 at 1:21 AM Mario Fernández Pendás <
> > mariofp77 at gmail.com>
> > wrote:
> >
> > > Dear all,
> > >
> > > Due to the computational facilities that I can use I am running 5000 ps
> > > simulations with the villin headpiece system and I am trying to compare
> > the
> > > sampling efficiency of two different methods.
> > >
> > > Since for this short simulations, I am not able to observe the folding
> > > phenomena, what would you suggest me to see the difference in sampling
> > > between my two methods?
> > >
> > > Thank you very much.
> > >
> > > Best,
> > > Mario
> > > --
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