[gmx-users] How many times should I do Umbrella Sampling

[André Farias de Moura]

Hi Agnivo,

good overlap of histograms and a smooth pmf cannot be taken as evidences of
convergence. Some people would extend the simulations to prove that pmf
does not change appreciably with further sampling, while other people (as
your reviewer) would do extra independent pmf profiles to prove that all
profiles agree within a certain precision (and then the best profile would
be the average, preferably the Jarzynski average of those profiles). I
prefer the later, though I think that it is a matter of taste, as long as
you are able to demonstrate that a thorough sampling has been reached. How
many extra replicas you should do is something you should validate for your
system (5 replica is somewhat arbitrary).

Maybe you might want to take a look at our papers dealing with that:

J. Phys. Chem. B, 2013, 117 (24), pp 7324–7334
Phys. Chem. Chem. Phys., 2015,17, 3820-3831

I hope it helps.

Andre


On Wed, Jun 8, 2016 at 8:38 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Hello Users
>
> I did one umbrella sampling on a trajectory generated by a pulling
> simulation. There were 45 windows in my US and the PMF curve converged with
> good overlap of histograms.
>
> However the reviewer is asking for 5 US simulations from 5 pulling sims on
> the same system and wants the average free energy from those 5 sims. I was
> assuming that the bootstrap calculation takes care of the averages.
>
> If there is a proper explanation / reply for the reviewer please share.
>
> I am unsure as it takes a long time to do one US sim. I did another one for
> the same system but for a different pulling simulation and the result is
> almost identical. I think as my pulling code is same I am getting more or
> less same result.
>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090