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

[maria goranovic]

The box size is more than 10 nm, the simulations runs for longer than 100
microseconds.

the center of mass motion is removed by something like this:

nstcomm                  = 1
comm-grps         = Lipid W

i have also tried to do it for the entire system

I will give the recentering another attempt, and get back to you


On Thu, Nov 5, 2009 at 1:57 PM, XAvier Periole <x.periole at rug.nl> wrote:

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