[gmx-users] Study of sampling of villin headpiece

[Mario Fernández Pendás]

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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