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From: Dulal Mondal via AMBER <amber.ambermd.org>

Date: Tue, 17 Jan 2023 10:15:57 +0530

Dear Experts,

Thank you sir for your suggestion. I have calculated the center of mass

(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) ?

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 Mon Jan 16 2023 - 21:00:03 PST

Date: Tue, 17 Jan 2023 10:15:57 +0530

Dear Experts,

Thank you sir for your suggestion. I have calculated the center of mass

(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) ?

On Mon, Jan 16, 2023 at 11:59 PM David A Case <david.case.rutgers.edu>

wrote:

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Received on Mon Jan 16 2023 - 21:00:03 PST

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