Re: [AMBER] Velocity file output AMBER16

From: Korey M Reid <>
Date: Tue, 14 Feb 2017 19:39:04 +0000

Thank you David for confirming how file write-out is performed. And is there any way to include this in the manual for future users interested in utilizing velocity trajectories.

This can be a little confusing with the current write up, as can be seen by the first response, and in my case it results in strange values. Now by calculating the velocity by taking ( t-dt/2 + t+dt/2)/2 I get results that make better sense.

Thank you again! Always an excellent source of help!

Best wishes,

From: David Case []
Sent: Tuesday, February 14, 2017 6:10 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Velocity file output AMBER16

On Mon, Feb 13, 2017, Korey M Reid wrote:
> >From reading I found in old versions the discussion that the md
> >velocity files were written a half interval between coordinate
> >writeout. Is this still true? If so, can I force amber to write out the
> >coordinates and velocities at the same time corresponding to the same
> >time?

I think this is still true, and that we indeed don't offer a way to write
coordinates and velocities at the same time step. The velocities you want
are indeed computed internally, so some energetic developer might wish to add
such an option, which would indeed be worth having.

Caveat: I may be missing something here, and if so, I hope people on the list
will correct me.


AMBER mailing list

AMBER mailing list
Received on Tue Feb 14 2017 - 12:00:02 PST
Custom Search