[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

XAvier Periole x.periole at rug.nl
Thu Nov 5 13:02:12 CET 2009

On Nov 5, 2009, at 12:09 PM, maria goranovic wrote:

> Hello All (and especially Berk)
> This is an update of the problem that I was facing earlier. I used  
> to tau_p of 3.0 ps, and the problem does not go away, the bilayers  
> still drifts in the simulation box.  So this is probably a bug then?
How much is the drift (nm/ns)? Did you use removal of center of mass  
of the entire system of
bilayer/solvent separately?
> I still cannot understand how to put the bilayer back into the  
> center of the simulation box. As suggested by Justin, I tried to use  
> just one tail atom of a lipid for centering, but that did not work  
> either.
> I noticed that my bilayer, which is initially at the center of the  
> simulation box, separates into two leaflets at the box edges from  
> the very first step of the simulation itself, but i am not able to  
> correct that using the -center and -boxcenter zero options. Can  
> someone please make a suggestion and help?
You have to do use -pbc nojump first and then center ...
> Thank you so much
> -Maria
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
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