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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Wed, Sep 3, 2014 at 6:38 PM, Shan-ho Tsai <tsai.hal.physast.uga.edu> wrote: > > David, > > Thank you very much for your response and your insightful > comments on such energy decompositions, I really appreciated > it. > > Thanks! > Shan-Ho > > ----------------------------- > Shan-Ho Tsai > GACRC/EITS, University of Georgia, Athens GA > > On Wed, 3 Sep 2014, David A Case wrote: > >> On Wed, Sep 03, 2014, Shan-ho Tsai wrote: >>> >>> I have just installed the serial version of Amber14 >>> (with updates 1 to 5 installed) and AmberTools14 (with >>> updates 1 to 11 installed) using the gnu 4.7.1 compilers >>> on our Linux cluster (64-bit RHEL5). All Amber14 tests >>> passed, but the sander_pbsa_decres test in the AmberTools >>> test suite failed (all other AmberTools tests passed). >>> The differences from the output file provided are very >>> large (see below). >> >> Thanks for the report. We are aware of this, and the bug is entered into >> bugzilla (bug #282). It's been a busy time, and no one has yet been able to >> track it down. If you plan to look a decomposition of PB energies, you should >> take care. >> >> ....dac >> >> [General caveat about such energy decompositions: (1) they are approxiate >> and somewhat arbitrary; (2) if you decompose numbers enough different ways, >> you increase your chances of being fooled by finding some combination of terms >> that appears to explain some trend.] >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Sep 19 2014 - 10:30:03 PDT