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

Stefan Hoorman stefhoor at gmail.com
Mon Sep 21 17:51:31 CEST 2009

2009/9/21 <gmx-users-request at gromacs.org>

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> Stefan Hoorman wrote:
> > I have a test set which is comprised of the same constituents of my real
> > system, except the solvent (i mean, it is in vacuum. This test set I use
> > to (as the name says) test different different parameters without having
> > to wait too much. I know it would not serve as a very quantitative set,
> > but even though, when I changed the force_constant of the umbrella
> > potentia to a lower value (from 35 to 10) I got something out of the
> > WHAM that looked more like a "rollercoaster", I little bit edgy perhaps,
> > but at least not a downstream line like the one before. When I changed
> > it again to 5 kJ, the graphic still looked like a rollercoaster but it
> > differed in 1 or 2 kcal more negative than the one with 10 kJ as
> > umbrella force constant. Perhaps, in addition to space my intervals as a
> > function of distance, my spring constant is wrong. Does that make any
> sense?
> Well, a "vacuum" run might be a bit strange, anyway, so I wouldn't base
> much on
> it, since the force fields weren't designed for that kind of usage.  Rough
> edges
> and transitions might be present, but could be smoothed with proper
> sampling and
> window distribution.  As for the force constant, I generally see much
> greater
> numbers in the literature (500-1000 kJ mol^-1 nm^-2).  I don't know if
> there's a
> rule of thumb for assigning this value.
> > Ahh...by the way, the link for oldwiki is not working. I will try it
> later.
> >
> Indeed, it has been running very slowly, at least.  You can access the same
> content here:
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
> -Justin
> 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?
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?
Thank you
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