[gmx-users] freezing/position restraints and minimization

Robert Johnson bobjohnson1981 at gmail.com
Fri Mar 16 22:03:05 CET 2007

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.

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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