[gmx-users] Re: Re: Re: Re: Re: Re: Re: umbrella potential

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 25 01:28:19 CEST 2009

Stefan Hoorman wrote:

> Hi again. I have finished my wham analysis and here is what came out. 
> Well, first let me remind you of what we have already talked about. I 
> have simulated my system, comprised of protein and ligand, with the pull 
> code set to umbrella in order to obtain the entry structures for the 
> sampling simulations for my wham analysis. Now, after several 
> suggestions I have finally come up with a set of parameters that seemed 
> to work. I have included the "pull_start = yes " in my windows' 
> parameter  file and have also increased the "pull_force" from 35 to 
> 2000. This increase seems to be sufficient to maintain my structures 
> restrained in the initial position, so now my distance between groups 
> float around a given value, which is quite close to the initial one. The 
> structures obtained for the wham windows were obtained selecting frames 
> in which a given distance between the structures was met. The structures 
> were obtained with a 0.1nm distance delta.
> The problem now is the following. According to my .edr file, I should 
> have no more interaction (LJ-SR and Coul-SR) between my structures 
> starting from 2.5nm distance between them. So I would expect that my 
> profile.xvg file resulting from g_wham would give my values that would, 
> from 2.5nm on, kind of stabilize. My profile.xvg resulting from g_wham 
> gives me increasing values of umbrella potential starting in -1.1kcal 
> mol\S-1\N until +90kcal mol\S-1\N.
> It does not look like anything I have seen for similar studies on the 
> literature. It has no minimum valey, i.e., the minimum value is the 
> first one and then the values just increase from there.
> Thank you

How long are you sampling in each window?  How many total windows do you have? 
What do the histograms look like?


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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