Hello,
I have been recently wondering about benefits of the AMBER program compared
to other software solutions (e.g., NAMD, Gromacs).
I myself first used Gromacs since 2002 to 2010, and then moved to NAMD
because I wanted to make parameters for new ligands and this was tricky
with OPLS but a lot easier for AMBERFF which was compatible with free NAMD.
Then I finally moved to AMBER program and use it since 2014, mainly to
benefit from the GPU-acceleration. However, since then many things have
changed with all the three programs, in particular they all support
AMBERFFs and have GPU implementations.
A recent book gives a short overview on the different programs (
http://www.springer.com/series/7651, Chapter 1) but despite the 2016 year
of publication it seems a bit outdated with citations up to 2014 and
talking of GPU implementations as of something that is yet to come.
So, could you recommend some recent publications on the topic?
And could you also answer some questions below based on your experience:
1. My understanding is that AMBER is not the fastest implementation, i.e.,
the GROMAC's GPU version of classical MD is significantly faster, right?
2. What about the implementation of the force fields?
- Both GROMACS and NAMD support the AMBERFFs, is there any difference in
how they do it compared to the original AMBER?
- Do the third-party programs support all AMBERFFs, including the most
recent ones (e.g., FF15IPQ)?
- I.e., are there any concerns about the third-party programs implementing
the AMBERFFs "incorrectly"?
3. What would you say about functionality (i.e., the number of different
methods) of GROMACs, NAMD and the AMBER program?
4. Why do you use the AMBER program? Do you use solely the AMBER program or
in a combination with other programs (i.e., AMBER for one purpose, NAMD for
the other purpose)?
Thanks for your time,
Dmitry
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Received on Fri Mar 23 2018 - 04:30:02 PDT
