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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 21 22:29:14 CEST 2009

Stefan Hoorman wrote:
>     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.
>     Justin
> Ok, here is what I meant. I use each of the starting position extracted 
> from my original pulling trajectory (i mean the trajectory with 
> "pull_rate  =  0.01") to simulate each window. Each of these windows 
> still have the umbrella force constant (pull_k1 = 35) but now have 
> "pull_rate = 0". My system, though, does not fluctuate about a mean 
> position in each window. My system returns to the initial dimer or tries 
> to if the distance is too big and the simulation time not long enough. 
> So, whem I analyse the distance between the two groups with g_dist in 
> each of the sampling windows, I get a series of decreasing values that 
> will eventually return to the 0.9 nm.
> For these simulations, I keep the same parameters as in the original 
> pull trajectory. The vectors are still the same, the force constant is 
> still the same. I only change the "pull_rate" from 0.01 to 0 and 
> "pull_geometry" from direction to distance (because g_wham asks tells me 
> "pull_geometry = direction" is not supported).
> So maybe I am doing something wrong.

If the starting structures are not staying in the desired windows, it seems to 
me that your force constant is not large enough to maintain these positions. 
Try something larger, like 500 or 1000 like I suggested before and see if you 
get a better result.


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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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