Re: [AMBER] Water Density

From: Seibold, Steve Allan <>
Date: Tue, 2 Oct 2018 12:57:30 +0000

Thanks for your response..of course, that makes perfect sense and also, thanks for info on parmed...that helps too...

From: David Case <>
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

AMBER mailing list

AMBER mailing list
Received on Tue Oct 02 2018 - 06:00:02 PDT
Custom Search