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

Stefan Hoorman stefhoor at gmail.com
Tue Sep 22 16:14:05 CEST 2009

2009/9/22 <gmx-users-request at gromacs.org>

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> > 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
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