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

Stefan Hoorman stefhoor at gmail.com
Mon Sep 21 22:11:14 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.
> 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.
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