This is all with the QM/MM module in sander and the QM region is the entire
system (a TIP3P water, but that shouldn't mean anything since all of the MM
terms are zeroed out). The SQM forces also come directly from the SQM
output (in au).
On Tue, Jan 28, 2014 at 10:57 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> related thread: http://archive.ambermd.org/201209/0554.html).
>
> 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
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ 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 - 08:30:02 PST
