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

Stefan Hoorman stefhoor at gmail.com
Fri Sep 25 04:53:37 CEST 2009

> > Hi again. I have finished my wham analysis and here is what came out.
> > Well, first let me remind you of what we have already talked about. I
> > have simulated my system, comprised of protein and ligand, with the pull
> > code set to umbrella in order to obtain the entry structures for the
> > sampling simulations for my wham analysis. Now, after several
> > suggestions I have finally come up with a set of parameters that seemed
> > to work. I have included the "pull_start = yes " in my windows'
> > parameter  file and have also increased the "pull_force" from 35 to
> > 2000. This increase seems to be sufficient to maintain my structures
> > restrained in the initial position, so now my distance between groups
> > float around a given value, which is quite close to the initial one. The
> > structures obtained for the wham windows were obtained selecting frames
> > in which a given distance between the structures was met. The structures
> > were obtained with a 0.1nm distance delta.
> > The problem now is the following. According to my .edr file, I should
> > have no more interaction (LJ-SR and Coul-SR) between my structures
> > starting from 2.5nm distance between them. So I would expect that my
> > profile.xvg file resulting from g_wham would give my values that would,
> > from 2.5nm on, kind of stabilize. My profile.xvg resulting from g_wham
> > gives me increasing values of umbrella potential starting in -1.1kcal
> > mol\S-1\N until +90kcal mol\S-1\N.
> > It does not look like anything I have seen for similar studies on the
> > literature. It has no minimum valey, i.e., the minimum value is the
> > first one and then the values just increase from there.
> > Thank you
> >
> How long are you sampling in each window?  How many total windows do you
> have?
> What do the histograms look like?
> -Justin
> I simulate 400 ps for each window. I have a total of 20 windows. My
histogram looks like a chromatographic peak ranging from 0.74 and 0.91 in
the x axis and the count (y axis) goes up to 30000. Is there a way to index
my histogram.xvg or my profile.xvg file and send it to the gromacs user's
list? Or is it not necessary?
Thank you
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090924/ab3774c0/attachment.html>

More information about the gromacs.org_gmx-users mailing list