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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 Nov 23, 2014, at 9:30 PM, Andreas Goetz wrote: > Dear Aixiao, > > Your general simulation setup sounds reasonable (if your QM method is able to describe proton transfer well). The problems you see might be related to a bug in the released version of the adQM/MM implementation. Could you please send me your input files off-list so I can check what is going on? Thanks. > > 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 Nov 20, 2014, at 2:32 AM, Aixiao Li wrote: > >> Hi, >> I am working on a system that bulk solvent participates directly in a proton transfer reaction. So the adaptive solvent QM/MM is a perfect solution. My goal is to run umbrella sampling with adQM/MM and do potential of mean force (PMF) study. >> >> So basically the whole story is adQM/MM umbrella sampling with nmr constraints on "O" (from my reactant) and "H" (from one bulk water) distance, let us say, windows from 2.0 ang to 1.0 ang. >> >> But while running simulations, as I define my reactant+7H2Os as my A region (with one H2O as my proton donor candidate) and 5 waters in the T region, the simulation behaves well for several time steps, but sometimes it appears >> "vlimit exceeded for step..." and the calculations keep going on. And the calculation could stop with error message like: >> >> "Coordinate resetting (SHAKE) cannot be accomplished, >> deviation is too large >> NITER, NIT, LL, I and J are : 0 4 20 80 78 >> >> Note: This is usually a symptom of some deeper >> problem with the energetics of the system. >> >> Is this because that my T region is not big enough or too big? I checked the configuration with VMD, and I could not find out anything strange, there is no hydroxide or hydronium ions formed... >> >> thank you very much >> >> >> best >> >> _______________________________________________ >> 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 Mon Nov 24 2014 - 14:00:04 PST