membrane system

From: ipsita basu (
Date: Wed Sep 21 2011 - 01:30:00 CDT

Sorry to disturb you again but I sent you mails before regarding this
problem but didn't get any reply from your end.
I have a membrane monolayer system, to make stable this monolayer I
use vaccuam, and to do this I twice the length of the simulation box
in z direction(membrane normal axis> in cellbasis vector option. But
after 8 to 10 ns the waters are again jumping to the lipid end. Will
you please tell me how to fix this?
Another question is if I use 2D option in cellbasis vector, the can
avoid the water jumping problem, but using 2D it will not be possible
to use PME. Is it okay to run without using PME?
Any kind of help from your end is really needed.
Thanking you,

Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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