Re: [AMBER] Setting initial velocities

From: David A Case <>
Date: Wed, 9 May 2018 08:27:58 -0400

On Tue, May 08, 2018, Hai Nguyen wrote:

> > I want to perform a free simulation in which the initial velocities of
> > a certain atoms are particular vectors to be specified by me. Is there
> > any simple way to achieve this?
> >
> > More specifically, I want to manually set the initial values of the
> > projections over certain directions of the velocites of my atoms of
> > interest.

Sounds like you should create a formatted restart file, and write a
script (in some language) to edit the values of the velocities, and
write a modified restart file. The file format for a restart file is
quite simple:, and the nature of your
request suggests that a specialized script will be needed.

If you are comfortable with Python, Hai's suggestion is a good one: with
that interface, you don't have to worry about file formats.

> >
> > The Amber rsmd files are awful to deal with, and I'm guessing there
> > should a simpler way to do this sort of things?

It's not clear (to me) what rmsd file have to do with getting modified
initial velocities.

...good luck....dac

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Received on Wed May 09 2018 - 05:30:05 PDT
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