Re: [AMBER] adQM/MM vlimit exceeded problem

From: Andreas Goetz <agoetz.sdsc.edu>
Date: Sun, 23 Nov 2014 21:30:49 -0800

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 
> 
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Received on Sun Nov 23 2014 - 22:00:02 PST
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