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

[Justin A. Lemkul]

maria goranovic wrote:
> I did use -pbc nojump, but that does not help
> 

What about entering on a central lipid tail atom, I suggested some time ago? 
The bilayer probably just splits across periodic boundaries, so this is not 
really a problem; just a visualization artefact.

-Justin

> The drift is about 1 nm per 10 microseconds .
> 
> (this is a martini simulation)
> 
> On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <x.periole at rug.nl 
> <mailto: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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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