Re: [AMBER] Center of mass, velocity, Momentum calculation

From: Daniel Roe via AMBER <amber.ambermd.org>
Date: Tue, 17 Jan 2023 13:05:17 -0500

Hi,

On Mon, Jan 16, 2023 at 11:46 PM Dulal Mondal via AMBER
<amber.ambermd.org> wrote:
> (COM) of HIS-64 using vector command. can I try to calculate the velocity
> of the COM using the dr/dt equation. Is it correct If I calculate the
> velocity using differential equation (dr/dt) ?

In general I would say probably not unless your trajectory write
frequency is very close to your time step. Otherwise the velocity
approximation will likely be too rough. I know from experience for
example that a velocity autocorrelation function calculated using
actual on-step velocities starts to differ quite a bit between actual
and approximated velocities as the trajectory write frequency
increases (although maybe thats a bad example since the VAC fxn needs
a fairly high write frequency to be useful anyway). Perhaps others
have a different perspective.

-Dan

>
> On Mon, Jan 16, 2023 at 11:59 PM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Sun, Jan 15, 2023, Dulal Mondal via AMBER wrote:
> > >
> > >I have a trajectory file (nc file) which contains only position
> > information
> > >but no velocity information.
> >
> > >1) How can I calculate the center of mass (COM) of a particular residue
> > >(HIS-64)?
> >
> > In cpptraj, two linked statements should do the trick:
> >
> > vector his64com center :64 # computes the center of mass of residue
> > 64
> > run
> > writedata his64.crd vectraj his64com trajfmt crd noorigin
> > #writes out the center of mass coordinates for residue 64 at each
> > # frame of the trajectory to the file his64.crd
> >
> > >2) How can I calculate momentum?
> >
> > Without having velocities, you can't get at momenta.
> >
> > ...good luck...dac
> >
> >
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Received on Tue Jan 17 2023 - 10:30:03 PST
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