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

Stefan Hoorman stefhoor at gmail.com
Fri Sep 25 01:01:53 CEST 2009

> >
> > > I will ty Justin's suggestion. I should have the answer by tomorrow.
> > > As for Thomas' suggestion, well, my mdp file didn't even have the
> > > "pull_start" flag. So I assume gromacs though I had set it to "no". But
> > > anyway, I checked the force in each window as you mentioned andfound
> > > something quite strange. The original pull_pf.xvg file, is an eve
> > > increasing line starting at -43 kj/mol/nm. So when I check a specific
> > > time frame, the pull force is, for example 93 kj/mol/nm at time frame
> > > 4000. But when I checked the pull force on the pull_pf.xvg file at that
> > > specific window, well, the pull force was something around -42
> > > kj/mol/nm. Now I am really confused. It seems I am doing something
> > > really wrong, but actually quite simple to solve. I will try setting
> > > "pull_start = yes" and see what happens.
> >
> > Because you're looking at two entirely different things.  In your initial
> > pulling simulation to separate your species, the force will continually
> > change,
> > building up until the two dissociate, then probably level off to some
> > roughly
> > constant value until the simulation stops (when the species are no longer
> > interacting).
> >
> > In umbrella sampling, the force imposed on the pull group is used to
> > restrain it
> > within a window, and will not necessarily have anything to do with the
> > values
> > obtained in the original separation simulation.  Apples to oranges, if
> you
> > will.
> >
> > Setting "pull_start = yes" is appropriate for the umbrella sampling.  In
> > conjunction with "pull_init1 = 0" the original distance between the two
> > species
> > should be taken as the distance to be restrained during umbrella sampling
> > simulations.
> >
> > > One other thing. I checked my pull_px.xvg file for the initial
> > > separation trajectory. It looks like a a rollercoaster with a tendency
> > > to going down. So the final value of distance PULL_COM is 1.5nm lower
> > > than the initial value. The values on each of my windows are the same
> > > for the individual values pf the separation trajectory from which they
> > > were taken. And again, the values on the pull_px,xvg files all
> decrease.
> > >
> >
> > Not a steady increase as the two species separate?  Is your box size
> > sufficient
> > to accommodate the distance you are pulling, or are you experiencing
> > periodicity
> > artefacts?
> >
> >
> > I am sorry. Correcting. The px values increase for my simulation. The
> files
> I checked were for a simulation with a smaller box periodicity does occur.
> With my actual system (larger box) the px values increase. I have started a
> new run for my windows setting "pull_start = yes" with "pull_init1 = 0".
> Once I have some of the simulations finished I should have an idea of what
> is happening.
> Thank you
> 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
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
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