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
Received on Thu Nov 20 2014 - 03:30:03 PST
