The crash seems to be expected as by crossing the pbc the distance
will change significantly
and in way the algorithm can not handle.
Note that the overall translational motion of your system should
always be removed.
The removal of the COM motion of your bilayer should be sufficient to
prevent the overall
motion of the bilayer. have a look at the following option in the mdp:
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = membrane solvent+ions
On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote:
Hi all!
I have a problem regarding lipid bilayer simulations in Gromacs 4.
During some of my simulations the whole system is moving in the z
direction in the box, meaning that after some time the lipids are
going out in the bottom of the box and coming in in the top of the
box, since I'm using periodic boundary conditions. This doesn't
matter (I think) when running non-constrained simulations, however
when I'm constraining the distance between the lipids
(pull_geometry=cylinder) and a molecule in the system the system
explodes and the simulations crash when the lipids are starting to
cross over to the other side. The fact that the system is moving in
the box must be the problem since the system explodes exactly when
the first lipid passes over to the other side and nothing like this
ever happens when the bilayer is not moving in the box. Is there any
way to freeze the cylindrical COM of the lipids or something like
that so that they stay more or less in the middle of the box all the
time? I don't want to use freezegrps and freezedim = N N Y as this
freezes the lipids completely in the z direction, and that's not
what I want, I want them to be free to move as before but I want to
stop the whole system from moving too much in the z direction.
Anyone that has experienced a similar problem or know how to go
about with this? I would really appreciate any help I can get. Thanks.
Emma
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