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

[maria goranovic]

I did use -pbc nojump, but that does not help

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> 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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>
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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