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

[XAvier Periole]

On Nov 5, 2009, at 1:43 PM, maria goranovic wrote:

> I did use -pbc nojump, but that does not help
It should! you do nojump and then center using the membrane only as a  
group reference.
f this does not work translate your trajectory first on the z axis by  
about one nm.
It is actually strange that 1 nm derive on the z axis get your bilayer  
from the
middle of the box to half out ! This would imply that your box is  
about two nm
high! This is smaller than the thickness of a bilayer!
>
> The drift is about 1 nm per 10 microseconds .
this is quite lot
>
> (this is a martini simulation)
This should not make a difference.
I also noticed that the removal of the COM is not done properly and on
a long run there are deviations ... smaller than the one you report but
still.

how did you remove the COM?
>
> On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> 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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>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
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