[gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

XAvier Periole x.periole at rug.nl
Tue Apr 27 13:41:39 CEST 2010

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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