On Thu, 2014-05-22 at 14:49 +0200, Soumendranath Bhakat wrote:
> Just a request, I noticed that there is no details of Amber tutorial on
> hybrid QM/MM method expect only one tutorial. Some components like what
> qmtheory will be used for what level of Qm is also not there. Say for
> example I use a DFTB-SCC level I will give qmtheory=7 so many people might
> use some other QM level but it is not in that tutorial.
I think you have missed the point of the tutorials. At the very top of
each tutorial is the following disclaimer:
(Note: These tutorials are meant to provide illustrative examples of how
to use the AMBER software suite to carry out simulations that can be run
on a simple workstation in a reasonable period of time. They do not
necessarily provide the optimal choice of parameters or methods for the
particular application area.)
The purpose of the tutorials is getting you comfortable with using the
software. Listing available Hamiltonians and different options is a job
for the manual and suggestions about which Hamiltonian to select and how
to partition the QM and MM parts of your system are left to literature
searches (the manual is a good source of references to start with) and
user experience.
> Also the QM/MM tutorial is no that much developed compared to other
> tutorials. This discussion is nice one. Will it be possible to update the
> QM/MM tutorial with new updates mentioning possible errors and other
> necessary points.
I don't see how it is "less developed" (outdated, sure -- nobody needs
warnings against using Amber 8 these days, especially when sander 14 is
free). I think it seems to meet its target objective (i.e., an
illustrative example that can be run on a simple workstation in a
reasonable period of time).
I also don't think that adding common pitfalls is really appropriate for
a tutorial (do many people go back to a tutorial as a reference if they
get an error in one of their calculations?)
Just my opinion, anyway...
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 22 2014 - 07:00:02 PDT
