Re: Velocity unit ofvelocity in NAMD the binary files

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Jun 14 2006 - 18:13:49 CDT

On Tue, 13 Jun 2006, Amin R. Mazloom wrote:

> Hi, Does any body knows what is the unit of velocity in the NAMD output
> file (.vel) ? it it Angestrom per femto second, Angestrom per time step
> or something elase ?

In the text (pdb) format it's Angstroms/ps, in the binary format it needs
to be multiplied by PDBVELFACTOR = 20.45482706 to get A/ps.

To see the actual code, search for PDBVELFACTOR on
http://www.ks.uiuc.edu/Research/namd/doxygen/Output_8C-source.html

Here's an explanation from
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0497.html

Mass is in amu, position is in Angstroms, and velocity is in internal
units. In short, multiply by 20.45482706 to get amu*A/ps or amu*A^2/ps.
Here's a long and nasty LaTeX explanation of the velocity units:

Energy is expressed as kcal/mol and hence force as kcal/mol/\AA. In order
to obtain \AA\ after multiplying forces by the timestep twice, the
timestep is divided by TIMEFACTOR = 48.88821. This number is the inverse
of the square root of the converstion factor for changing from units of
(kcal fs$^2$)/(mol \AA\ amu) to \AA\ (which is {\em exactly} $4.184 \times 10^{-4}$ assuming thermochemical calories).

The timestep in DCD files is already divided by TIMEFACTOR, so converting
it to ps is simply a matter of multiplying by 48.88821.

Velocities may be converted to something useful like \AA/ps by first
multiplying by TIMEFACTOR to obtain (kcal fs)/(mol \AA\ amu) and then
converting this quantity by multiplying by $4.184 \times 10^{-1}$. If
TIMEFACTOR were calculated exactly, the total conversion factor would be
20.45482828. With the given value of TIMEFACTOR as used in the code, the
value is 20.45482706 instead. This conversion is applied when velocities
are written to a text PDB file, but not for binary restart files.

-Jim

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