On Mon, Dec 09, 2002, Prabal Maiti wrote:
> When I use amber7 on to continue my dynamics runs I get different energy
> compared to amber6 runs. Can someone suggest which parameters (default
> etc) needs to be specified to get exactly same energy. The inital energy
> is same in both amber6 and amber7. But during the dynamics energy differs.
See point (3) on p. 4 of the Users' Manual. Basically, with ntt=0 you
should see no differences over short trajectories; for example, the dhfr
and jac benchmarks give identical results for amber6 and amber7.
> Also how accurate is PME. In amebr6 run I had nfft1=45 and in amber7
> nfft1=48 (it does not accept odd number) and the electrostatics energy is
> different by 100 kcal/mol though the change is less than 1%.
I gather this is a different problem(?), since the example you quoted in
your mail had identical electrostatic energies.
Sander 7 has instituted a faster (but equivalent) way of doing the reciprocal
sum. A side effect of this was to disallow odd values for NFFT1 (for
convenience in coding, no fundamental reason.) You could relax this by
defining -DnoRCFFT in your MACHINE file and re-compiling. Mike Crowley may
also know some other work-around (if I remember correctly, NFFT2 and NFFT3
can be odd...)
I agree that a 1% change seems pretty big, but I haven't tried test cases
myself. Take one of the benchmarks or test cases (say dhfr) and experiment
with changing the grid spacing slightly. Again, maybe others will have good
comments.
..regards...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Dec 11 2002 - 07:40:48 PST
