Thanks for your response..of course, that makes perfect sense and also, thanks for info on parmed...that helps too...
Steve
________________________________________
From: David Case <david.case.rutgers.edu>
Sent: Monday, October 1, 2018 6:32 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Water Density
On Mon, Oct 01, 2018, Seibold, Steve Allan wrote:
>
> I am trying to obtain the water density after my minimization (NPT)
> steps to verify that I have the proper density but I cannot find it in
> the log print out or how to obtain it using some module in AMBER..Is
> there an straightforward way to obtain this info? I looked online but I
> could not find the answer..
Only molecular dynamics "knows about" pressure, since it is only with dynamics
that one has kinetic energy that is a key ingredient in computing the
pressure. Minimization never changes the box size, and is not NPT. Hence,
you won't find any such information in a minimization run. The density will
be unchanged from the initial value. (You can use "summary" command in parmed
to compute the density of the system.)
...good luck....dac
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Received on Tue Oct 02 2018 - 06:00:02 PDT
