On Sun, May 3, 2015 at 12:10 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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.
>
I can add it to my Wiki if it's of interest, but it's an awful lot of
headache to go through for just doubling the speed of sander (compared to
the more-than-an-order-of-magnitude boost you get from GPUs, which will not
work with Amber 11).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun May 03 2015 - 17:30:03 PDT
