[gmx-users] freezing/position restraints and minimization
dmobley at gmail.com
Fri Mar 16 22:21:05 CET 2007
OK, further info on this. Looks like it's the minimizer, at least in
the case of freeze groups. I'm using l-bfgs; it seems the minimizer
doesn't respect the constraints imposed by freeze groups.
Now that I think of it, I seem to remember that most of the minimizers
in GROMACS don't respect constraints. I think I'll try again with only
a steepest descents minimization (I think steep works OK with
constraints, if I remember correctly) and see if this helps.
On 3/16/07, David Mobley <dmobley at gmail.com> wrote:
> > Maybe this is a stupid suggestions but....did you check if your two
> > atoms are centered in the box and that the box dimensions are big
> > enough to accomodate your system? Maybe the atoms appear to be "flying
> > apart" because periodic boundary conditions are being applied.
> They're not "flying apart" in a ridiculous sense -- i.e. box
> dimensions are a couple nm, and the distance between them goes from
> 0.14 nm up to 0.25-0.28 nm. Also, I used g_dist to measure the
> distance between them; it takes care of all the PBC wrapping. So no,
> that's not what's going on.
> One possible complicating issue is that the atoms in question right
> now are two carbon atoms and I'm trying to hold them at the typical
> carbon-carbon bond distance, so they are sort of up against each
> other. So I can buy it might take a big force constant to keep them
> from moving apart -- I just can't figure out why freeze groups isn't
> working. (Incidentally, if I look at a movie of the trajectories run
> with freeze groups, it does look like they stay frozen -- just not at
> the positions I've specified).
> > On 3/16/07, David Mobley <dmobley at gmail.com> wrote:
> > > All,
> > >
> > > I'm trying to be ultimately able to fix the position of several
> > > arbitrary atoms (think of them just as spheres) in a simulation. One
> > > would think this should be straightforward, but I'm having big
> > > problems.
> > >
> > > In particular, right now I'm just using two atoms, which I initially
> > > have at a separation of 0.14 nm (i.e. one is at 0,0,0; the other at
> > > 0.14, 0, 0). I have tried freezing the positions in two ways. First, I
> > > tried using freeze groups, with the two atoms defined as a single
> > > group, specified in my mdp file, using freezedim= y y y.
> > > Unfortunately, as soon as I even minimize the system (with freeze
> > > groups on!) they fly apart to about twice the desired separation and
> > > stay further apart throughout dynamics (at least as measured by
> > > g_dist).
> > >
> > > I've also tried using a position restraint file with the default
> > > spring constant to hold them at the desired positions, but that
> > > doesn't seem to work either (again, they end up at about twice the
> > > desired separation).
> > >
> > > Any ideas? Especially on why freeze groups might not be working --
> > > ideally I would just fix these in place using freeze groups, but for
> > > some reason that doesn't seem to be working properly.
> > >
> > > This is in 3.3.
> > >
> > > Thanks,
> > > David
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