[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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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