# Re: [AMBER] fun with units?

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 28 Jan 2014 10:57:54 -0500

On Tue, 2014-01-28 at 09:43 -0500, Brian Radak wrote:
> I'm having a difficult time converting the forces from a mdfrc NetCDF file
> to atomic units (I'm trying to use AMBER as an external call in Gaussian).
>
> All sources seem to agree that forces are stored in amu-A/ps^2 and then
> scaled by 1/20.455^2 (presumably related to internal use of kcal?).

It's Amber's internal time units converted to ps, squared.

> So I've
> extracted the forces and multiplied by 20.455^2. I thought the following
> would be true:
>
> g-A/mol-ps^2 * (1 kg/10^3 g) * (1 m/10^10 A) * (10^9 ps/1 s)^2 = 10^5 kg
> m/mol-s^2 = 10^5 N/mol
>
> and then I could simply multiply by au/N and divide by Avogadro's number.
>
> >From Google, etc. I find 1 au = 8.23872206138418e-08 N
>
> As a test, I minimized and performed a normal mode analysis on a water
> molecule using AM1 in Gaussian with both SQM and AMBER as external
> routines. I used a numerical Hessian routine and SQM matches the native g09
> AM1 geometry and frequencies to within 1 cm-1. However, the AMBER
> frequencies at the same geometry are off by a factor of ~35.56. If I scale
> the AMBER forces by yet another factor of 35.56^2 I then get near perfect
> agreement (within .1 cm^-1), even if I minimize with both programs
> separately (as opposed to using the same input geometry).

What water model are you using? The forces for any rigid model are
quite arbitrary since they need to be used with constraints, anyway (a

What about trying QM/MM using sander and get the forces from there to
see if there's some conversion problem rather than running SQM directly?
They should match...

Alternatively, try a flexible water model and see if the results
improve.

All the best,
Jason

```--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
```
Received on Tue Jan 28 2014 - 08:00:02 PST
Custom Search