[gmx-users] freezing/position restraints and minimization

David Mobley dmobley at gmail.com
Fri Mar 16 21:50:05 CET 2007


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

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

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.


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