[gmx-users] freezing/position restraints and minimization
bobjohnson1981 at gmail.com
Fri Mar 16 22:20:18 CET 2007
If they are at the carbon-carbon bond distance, then their van der
Waals radii will be overlapping and the force between them is huge.
You can turn off this interaction with energygrp_excl = atom1 atom2
(with atom1 and atom2 defined in your index file).
I'm not sure why your atoms would be moving when you are using freeze
groups. In my experience, the positions of the atoms in the freeze
group have remained completely fixed.
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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