[gmx-users] problem with undistribution of water

[Justin A. Lemkul]

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi gmx users,
> I inserted my protein into Popc Bilayer . EM is fine,  when I do
> equilibration the water molecules from oneside of bilayer moving to other
> side, it looks undistribution of water , but total sturucture in cubic form.
> can you give me detailed information regarding this problem
> is it due to pressure coupling?

I'm not sure I understand your question properly, but if you are seeing water
molecules move through the "bottom" of the system to the "top" of the system,
that is just PBC.  If your bilayer is leaking, that's an entirely different
problem :)

It would be useful if you described your system a bit more thoroughly (box
dimensions, what force field parameters you are using, how you inserted your
protein).  This will give everyone a better perspective on what you're doing
instead of having to guess.  Also, it would be _very_ useful in this type of
situation to post an image (.jpg, .png, etc) somewhere that we could all see
it, if you are willing to do so.

-Justin

>
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  Berendsen
> tc-grps             =  POPC   Protein   SOL_Cl
> tau_t               =  0.1     0.1      0.1
> ref_t               =  310     310      310
> ; Anisotropic pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  anisotropic
> tau_p               =  2.0      2.0     2.0     2.0     2.0   2.0
> compressibility     =  4.5e-5   4.5e-5  4.5e-5   0       0      0
> ref_p               =  1.0      1.0     1.0      0       0      0
>  pbc                = xyz
>
>
> Thanks in advance........
>



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Justin A. Lemkul
Graduate Research Assistant
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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