[gmx-users] small protein & big frozen group - exploding

Omer Markovitch omermar at gmail.com
Wed Nov 12 16:47:04 CET 2008

I am simulating a small protein (less then 50 amino acids) at room
temperature, with no additional atoms and/or molecules and/or ions. The
simulations seems to proceed ok (in terms of avg. kinetic energy and other
energy terms).
Then, I take the same protein, and introduce a "surface" to the system.
My surface is just a set of identical hard sphere atoms, here is how a
surface atom is defined inside my .TOP file:
 [ atomtypes ]
  ;name  mass     charge   ptype c6       c12
 X     1.000    0.000 X    0.000  0.600E-09
And there are 10 times more surface atoms then protein atoms.

In my .MDP file, there are two energy groups: protein & non-protein. The
surface is frozen in all xyz directions.
Now, the problem is that with the surface, my protein quickly explodes, and
I have no idea why. The surface and protein each coupled to its own

Your help and ideas/comments are appreciated. Omer.

Koby Levy research group,
Weizmann Institute of Science.
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