[gmx-users] Questions about water in Gromacs

Erik Marklund erikm at xray.bmc.uu.se
Thu Aug 24 02:53:43 CEST 2006

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" <Dallas.Warren at vcp.monash.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at 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
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9524
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
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