CGMD problem

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Tue Dec 02 2008 - 11:10:34 CST

Dear all:

        With many helps from people on the list, I now can run the
CGMD finally. Many thanks to you guys.

        But when I was checking the trajectory in VMD, a weird cavity
formed in my system, which is not supposed to happen. The system was
also going pretty wild( I attached one snapshot of the system, water
in bead rep, lipid and protein in bond rep)
        My questions are:
        1) I checked the CG POPC definition in the topology file and found 12
beads are used(4 for each lipid tail, and the other 4 for lipid head).
But if I remember correctly, the 2 lipid tails in POPC has different
number of carbons(1 with double bond has 18, and another has 16). So
can anyone explain why the exact same beads
are used for 2 quite different tails?
        2) Since I got the error "Unable to find angle parameter for Nxg Nxx
Nxg" when the simulation was started, I added the following parameters
into the CG parameter file:
        Nxg Nxx Nxg 2.988 92
        Nxg Nxg Nxg 2.988 92
        Is this reasonable?
        (I asked this question before but haven't got a complete answer yet.)
           Thanks a lot.
        My configuration file is also attached.
Bin

Configure file and snapshot LINK:
http://www.its.caltech.edu/~bingo/

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