Restart simulation of an equilibrated bilayer with sugar molecules inserted

From: Keller Wenger (kellerwenger_at_gmail.com)
Date: Sun Mar 17 2013 - 09:51:27 CDT

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Hi, everyone,

I have got a fully equilibrated DPPC bilayer system. I have .pdb, .psf,
.coor, .vel, and .xsc files able to restart the simulation for the DPPC
system. Now I need to insert several sugar molecules into water layers
above and below the bilayer. But I only have .pdb and .psf files for these
sugar molecules. So, how can I restart simulating such a combined system
without destroying the equlibrated DPPC system? Since it is only a minor
change to the whole bilayer system, I think I don't need to re-equilibrate
the integrated system from a scratch.

I can generate integrated .pdb and .psf files for DPPC+sugar, but I have no
idea how to generate integrated .coor, .vel and .xsc files.

Any suggestions would be really appreciated.

Keller

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