Sorry to ask the obvoius, but did you try to perturbe the ordered structure
of the water with some position restaints MD? Energy minimization? I might
have misunderstood, but the ordering you describe ("the water core seems to
be distributed evenly in the system") suggests that your system has been
subjected to neither energy minimization, nor euilibration.
/Erik Marklund
----- Original Message -----
From: "Dallas B. Warren" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Thursday, August 24, 2006 1:20 AM
Subject: RE: [gmx-users] Questions about water in Gromacs
Justin,
Have you simulated each of the components on their own, i.e. pure octane
or water?
That should help to start to pin down what the issue is, just take it
one part at a time.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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