[gmx-users] Study of sampling of villin headpiece

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 30 13:51:40 CEST 2015


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 ;-)


On Thu, Jul 30, 2015 at 1:21 AM Mario Fernández Pendás <mariofp77 at gmail.com>

> 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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