question on membrane simulation

From: Longzhu Shen (
Date: Tue Feb 07 2006 - 11:03:43 CST

Dear All,

I am using NAME to simulate the gp41 fusion peptide interaction with POPE. I
was wondering whether I need to solvat the model after inserting the peptide
into the lipid bilayer. Since the POPE model built from the membrane package
with water molecules on both ends, I think I do not need add more water in.
But when I tried position-restrained md after energy minimization, it gave
the following information and said margin was to small to partition the
system. Then I set this value to 8 increasingly to make md run, although
extremely slow.

ENERGY: 0 79.6035 1031.5629 1068.2365 4.9426
-15999.2418 -709.9323 0.0000 0.0000 -99999999.9999
-99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999 147220.5786 -99999999.9999 -99999999.9999

Could anyone tell me how to set the Margin value correctly? Many thanks.


Longzhu Shen

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