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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 21 19:02:28 CEST 2009

Stefan Hoorman wrote:

> I am starting again my calculations for the real system and this am 
> going to use as starting positions distances in intervals of 0.1nm. Some 
> of them aren't really 0.1nm apart since the distance between the 
> twogroups in my first trajectory does not always increase in a steady 
> way, but the average distance between them is close enough to 0.1nm. I 
> looked back in the mailing list and found something about applying 
> restraints to these simulation windows. I imagine these restraints refer 
> to the umbrella potential still on and not actual restraining as in 
> adding -DPOSRES, right?

Without a link to the post you're reading, I can't comment on that.  It probably 
refers to the umbrella biasing (restraining) force, but without context, that's 
just a guess.

> One other thing I've noticed is that the distance between my groups 
> decrease in several of my windows, as one would expect since the two 
> structures still interact with each other, and in some cases they get 
> back to the original distance prior to the separation. Is this normal 
> for the WHAM analysis?

I don't understand what you mean.  There should be some fluctuation about a mean 
position in each window.  The umbrella potential maintains this distance, on 
average, if you're doing things right.


> Thank you
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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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