[gmx-users] Creating a box of water with density 1000 g/l

Justin Lemkul jalemkul at vt.edu
Sat Sep 12 03:29:16 CEST 2015

On 9/11/15 11:46 AM, Ebert Maximilian wrote:
> Thanks for the reply. I think I can simulate it now. The only thing I don’t understand and this is in reference to my other post: OPLS/AA parameters for 2-propanol
> How can the self-diffusion coefficient be a good measure for testing my parameters if for TIP3P water the self-diffusion coefficient ist 6 x 10^-9 m2 s-1 but the experimental value is around 2.3 x 10^-9 m2 s-1. So if even for a highly used water model the coefficient doesn’t fit how can I make any assumption about the quality of my parameters for 2-propanol?

Just because one molecule has flawed parameters doesn't mean you shouldn't 
consider this as viable target data for other molecules.  Diffusion constant is 
but one of many properties you need to look at if you want a valid model of 
propanol (or any molecule) - neat liquid structure, density, diffusion, DHvap, 
dipole moment, etc.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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