Hi Yao,
> When I followed the QMMMMD tutorial by Ross Walker on Amber website, I
> found before running the final production
>
> MD run, there is no restrained/unrestrained energy minimization or
> restrained dynamics (sometimes the latter is called "equilibration
> dynamics" with its main purpose of assigning velocities to the system
> and bring the system from 0 K to the expected temperature). I was just
> wondering if it is the purpose of simplifying the tutorial that makes
> this skipping occur or it is just safe in both theory and practice to
> skip.
This is a VERY subjective decision based on the system you are simulating.
In the case of this tutorial it was skipped to simplify things since the
purpose of this tutorial was just to show the syntax needed etc to run a
QMMM MD simulation with AMBER.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Wed Oct 05 2011 - 15:30:03 PDT
