[gmx-users] Questions about water in Gromacs

[David van der Spoel]

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" 
> <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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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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