AMBER Archive (2009)

Subject: Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Mar 11 2009 - 06:08:17 CDT

On Tue, Mar 10, 2009, Jose Borreguero wrote:
>
> I am running NPT simulations and apparently the speeds of the hydrogens are
> systematically underestimated roughly by a factor of sqrt(2). I have checked
> with two different proteins and two different temperatures, having same
> results
>
> I am using the SHAKE algorithm, so I ignore how hydrogen velocities are
> estimated in this case.

Can you give more details:

1. How did you find out the velocities of the hydrogens?
2. How did you decide what it "should" be?
3. What happens if you turn SHAKE off? (As you point out, it is
complex to analyze velocities when constaints are present.)

...dac

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