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From: Brian Radak <radak004.umn.edu>

Date: Tue, 28 Jan 2014 09:43:19 -0500

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

Date: Tue, 28 Jan 2014 09:43:19 -0500

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.

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. _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jan 28 2014 - 07:00:02 PST

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