Alok wrote:
Dear Chris,
Thanks for your time and suggestion.
I tried all the possible pressure couplings (including semiisotropic)
and run it for around 500ps.Gap between head group and water molecule
disappear, but I was getting uneven distribution of water molecules. I
am pasting my previous mail again. Hope I will get any solution for my
problem.
Best Regards,
Alok
##############################################################
Dear Mark,
Thanks a lot for your valuable time, and sorry for inappropriate
description, I am describing again, I hope thin time I can make it clear.
I took preequilibrated POPE.pdb files which already have SPC water
molecules
I had deleted these water molecules
Why not leave them?
and change the box size at 'Z Axis'
only, so I can accommodate more water, then using genbox I had added TIP4P
water molecules, but it also added the water molecules in the interior of
the bilayer. So I deleted these water by the criteria if the 'Z' coordinate
of the water in between the 'Z_min' and 'Z_max' of 'C13' (where
branching of
the POPE molecules start) atom. After that I got the files which don't have
any water at the interior of the bilayer but there is a vaccuum between
lipid head group and TIP4P water molecules (I defined it as a ZONE in my
previous mail).
The Z-coordinate-based water-removal procedure you describe can't create
such a vacuum, so I can't follow your description.
As discussed in the mailing list so many times I can do
same
thing by increasing the VdW radius of lipid atoms. But after that I was
expecting these vacuum will be vanished and water molecules will spread
homogenously after sort span of MD, as suggested in the mailing list. But
here problem has started I run MD till 500ps, but water molecules are
clustered at some places, at some places there is no water or very less
water. i.e. I am getting uneven distribution of water molecules over lipid
head groups.
I'm afraid I can't understand what you mean by "uneven distribution" in
the absence of a picture or a structure.
So I thought this problem might be due to pressure coupling or type of
ensemble I am using (might be I am wrong here !).
I ran four different sort MD by using isotropic, semiisotropic, anisotropic
pressure coupling and last one no pressure coupling (NVT ensemble). But in
all the cases I am getting similar structure at last which is uneven
distribution of TIP4P water molecules over head groups.
I made suggestions about your parameters last time. You don't seem to
have followed them.
Mark
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