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-- Dr. Andreas W. Goetz Assistant Project Scientist San Diego Supercomputer Center Tel : +1-858-822-4771 Email: agoetz.sdsc.edu Web : www.awgoetz.de On Aug 1, 2013, at 9:26 PM, Fabrício Bracht wrote: > What about using the switching function along the high collision frequency? > I saw that the the default for amber is to use the upper boundary for the > switch function is qmcut and the lower boundary is the high boundary minus > 2. Would it be possible to set the switch upper boundary to qmcut + 1 and > the lower boundary to qmcut -1? > Thank you > Fabrício > > > 2013/8/2 Andreas Goetz <agoetz.sdsc.edu> > >> Jason's interpretation is correct, the adaptive QM/MM code is currently >> available to developers collaborating with us. I had planned to release it >> with AMBER 12 but did not have time to properly test the code. >> >> I would strongly advice against using a step function at the QM/MM >> boundary. In the very least one should use a switching function for the >> forces as in Rode's "hot spot" method (Chem Phys 211, 1996, 313-323). >> Although it is possible to keep simulations somewhat under control with >> Langevin dynamics and a very high collision frequency (large value of >> gamma_ln) and still obtain structural properties (for example RDFs of ions >> in water) that are comparable to adQM/MM simulations with Bulo's DAS >> method. See for example my talk from the 2011 ACS spring meeting >> http://awgoetz.de/data/agoetz_adqmmm_acs-anaheim_2011.pdf (slides 18/19 >> for step function, slides 28/29 for adQM/MM). >> >> All the best, >> Andy >> >> -- >> Dr. Andreas W. Goetz >> Assistant Project Scientist >> San Diego Supercomputer Center >> Tel : +1-858-822-4771 >> Email: agoetz.sdsc.edu >> Web : www.awgoetz.de >> >> On Jul 31, 2013, at 8:21 PM, Jason Swails wrote: >> >>> On Wed, Jul 31, 2013 at 3:05 PM, Fabrício Bracht <fabracht1.gmail.com >>> wrote: >>> >>>> HI Ross. I just read the paper describing the use adQM/MM in amber. It >> says >>>> there that the code has been implemented in amber, but you mentioned >>>> earlier that it will be a part of the next version of amber. I am >> guessing >>>> that the code that has been implemented is only available to developers, >>>> correct? >>>> >>> >>> The way I would interpret Ross's email is that adaptive QM/MM is only >>> developers. Variable solvent QM/MM is available in Amber 12. >>> >>> >>>> You also mentioned earlier the the discontinuity problems can be a >> problem >>>> if one does not use a very tight thermostat. By using langevin >> thermostat >>>> and a small gamma_ln value would I be able to use the adaptative scheme >>>> efficiently to include solvent effect on the qm region? >>>> >>> >>> The discontinuity is a problem of generic variable solvent -- a problem >>> that adaptive QM/MM solves by generating intermediate stages by which the >>> QM region is 'morphed' into MM continuously to avoid abrupt changes in >> the >>> potential that arises by swapping quantum water molecules. (At least >> that's >>> my understanding based on presentations I can remember). >>> >>> A small gamma_ln value would provide tighter temperature control and >>> _might_ stabilize vsolv=1 simulations. It may be worth trying. >>> >>> HTH, >>> Jason >>> >>> -- >>> Jason M. Swails >>> BioMaPS, >>> Rutgers University >>> Postdoctoral Researcher >>> _______________________________________________ >>> 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/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Aug 02 2013 - 11:00:04 PDT