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

[XAvier Periole]

you need to do:

1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z  
direction
2- trjconv -center; using the bilayer to center and the system as  
output; this will
translate your bilayer on the z axis and normally not modify it on the  
xy plan.
3- trjconv -pbc mol; will put your lipids in one piece in the box; I  
believe this
step cn be coupled to the previous quite safely.

On Nov 5, 2009, at 3:23 PM, maria goranovic wrote:

> One more note about -pbc nojump. I typically use -pbc mol. Using pbc  
> nojump succeeds in keeping the center of the bilayer at 0 0 0, but  
> the atoms have moved way out of the simulation box resulting in a  
> dilute system
>
> On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic <mariagoranovic at gmail.com 
> > wrote:
> Centering on one atom has a problem that the lipid diffuses in the  
> plane of the membrane, and as a result, the entire system starts to  
> center around the lipid resulting in a simulation box which  
> translates a lot in the bilayer plane.
>
> The splitting is not a problem, yes. But during the simulation  
> period when the bilayer is not split, it diffuses quite a bit along  
> the bilayer normal (after use of -pbc mol, and centering around the  
> lipid center of mass). a plot of the lipid center of mass shows the  
> bilayer diffusing along z, when its not split.
>
>
> On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote:
>
>
>
> 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.
> The splitting is not a problem and I think that centering using one  
> lipid (tail) won't change the problem if
> the bilayer is cut half! Or the -pbc mol should be applied ...
>
>
> -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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>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
>
>
>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
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