[gmx-users] Re:density of the bilayer

minnale minnale_gnos at rediffmail.com
Wed Nov 12 18:40:08 CET 2008

Thanks alot for your reply

> > In case of water density, starting of the water density will be for some
> >time should come straight line in the graph later gradually reducing and goes
> >to zero towards centre of the bilayer again it increases and stop going the
> >water density.
> >
> > but in my case starting water density itself reducing gradually instead of
> >coming straight line for while.
> > is my opinion wrong?
>Ok there you seem to be right.
>Do you actually do the density only on water? You should give an index to
>g_density and choose from it the water or something else.

I have calculated density for all groups seperately like phosphate, choline etc. but every group is fine except water density that's why I posted question to archives.

>Is your system centered? I mean the bilayer in the center of the z axis and
>therefore the water distributed on both sides.

How can we know that system is centered or not?

>Do you actually have enough water solvating your balayer and therefore
>showing this plateau value before the decrease?

I have taken popc structure form Dr.Tieleman's site and simulating contain 2460 water molecules

sorry for the asking trivial queries I am new to bilayer simulations

Any suggestions would be appreciated

Thanks in advance
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