question on membrane crushing

From: Longzhu Shen (
Date: Thu Mar 02 2006 - 15:18:09 CST

Dear All,

I was trying simulating the POPE membrane with namd. I manually inserted a
peptide into the POPE model, ran minimization, heated the system, performed
position restrained md and free md. Everything went with along the
simulation. However, when I checked the trajectories with VMD, I found the
water on the two ends both moved toward the middle of the system. This made
the two leaves of the POPE further inserted to each other and lipid bilayer
severely crushed. The energy of the system looked stable during the whole
process with VDW slightly less than zero. I'd attache the configuration file
and wonder whether any kind guy could point out where I made mistakes. Many


Longzhu Shen

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