Hi John,
Something else to consider here is that the equilibrium density of a
particular water model may not precisely match the density of physical
water (particularly if you are considering a range of temperatures).
You may want to consider this before comparing the density of an MD
system to experimental densities. Short NPT simulations of a box of
your particular water model would be an easy way to determine your
model's density at different temps.
-Hugh Heldenbrand
Grad student, UMN
On 01/18/2012 07:28 AM, Beale, John wrote:
> I need to adjust the density of my protein/explicit water system to match experimental density values at a variety of temperatures. From what I have read, to do this I should adjust the volume of the system. Can someone please tell me how to do this?
>
> John
>
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
>
>
>
>
>
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Received on Wed Jan 18 2012 - 06:00:08 PST
