Lipid bilayer center go away from center of system.

From: ghg_at_xalt.am
Date: Sun Jun 18 2006 - 10:10:38 CDT

• Next message: JC Gumbart: "Re: Lipid bilayer center go away from center of system."
• Previous message: Dong Luo: "Re: Compile NAMD on Bluegene"
• Next in thread: JC Gumbart: "Re: Lipid bilayer center go away from center of system."
• Reply: JC Gumbart: "Re: Lipid bilayer center go away from center of system."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

I have lipid bilayer - water system, which consist from 128 lipid
molecules, 64 molecules at each side. Starting system equilibrated and from each side of lipid
bilayer I have same quantity of water.
During simulation center of mass of whole system not changing(its
normall), but lipid bilayer center of mass slowly going down in z
direction, and on 20ns of my simulation on upper side there 2000
water molecules and on lower side 970 molecules.
I understand that WrapAll function enabled and water molecules
transfering over Periodic Boundary Box. But what is the physical reason for that type of transfer of lipid bilayer?
Additionally I attach simulation configuration file.

Thank's
Hrant Gharabekyan
Bioinformatic Group of National Academy of Science of Armenia

• application/octet-stream attachment: NPT.conf

• Next message: JC Gumbart: "Re: Lipid bilayer center go away from center of system."
• Previous message: Dong Luo: "Re: Compile NAMD on Bluegene"
• Next in thread: JC Gumbart: "Re: Lipid bilayer center go away from center of system."
• Reply: JC Gumbart: "Re: Lipid bilayer center go away from center of system."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:44 CST