On Sun, May 03, 2015, Atila Petrosian wrote:
>
> Should I do both of parallel installation and pmemd installation?
This depends on whether you have computers available to you with multiple
cores. Most computers do these days, so it is generally worth making a
parallel installation.
>
> Two general question : which of pmemd and sander.MPI is faster?
For a given number of cores, pmemd.MPI will generally be faster than
sander.MPI.
> which of pmemd and sander.MPI is more accurate?
Both give the same results.
>
> I want to do MM-PB(GB)SA in future. Which of pmemd and sander.MPI is more
> appropriate for me?
The "expensive" part of MM-PBSA is creating the solvated trajectory in the
first place. So what is worthwhile optimizing is the speed of "ordinary"
simulations.
My advice: if you are just beginning, don't worry about pmemd for now.
Use your AmberTools14 installation, and gain experience in running and
analyzing simulations. Later, you can return to the question of how best
to install pmemd. Basic instructions are here:
http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
but they won't work unchanged for you, since for some reason you can't get the
old AmberTools1.5 to build. I think I can persuade some deveoloper to work
up details of how to compile just pmemd from an old distribution (without
requiring a complete build of AmberTools), and use it alongside AmberTools14.
....dac
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Received on Sun May 03 2015 - 09:30:02 PDT
