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

[XAvier Periole]

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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