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?). 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).
Any ideas what I missed here? 35.56 is not close to any constant/conversion
I am familiar with and seems much to large to be accounted for by numerical
differences in constants (presumably there is an "AMBER consistent"
constant for au/N that is slightly different than the one above).
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Jan 28 2014 - 07:00:02 PST
