Erik Marklund wrote:
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
in addition you may have too much water, more than your micelle can contain.
----- 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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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phone: 46 18 471 4205 fax: 46 18 511 755
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