[gmx-users] Study of sampling of villin headpiece

[Mario Fernández Pendás]

Hi Mark,

Thank you very much for your suggestions. Trying dialanine sounds like a
good idea.

Best,
Mario


2015-08-03 14:11 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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