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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 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/amberReceived on Sun Nov 23 2014 - 22:00:02 PST