On Wed, Apr 22, 2015 at 12:18 AM, Atila Petrosian <atila.petrosian.gmail.com
> wrote:
> Dear Jason
>
> Thanks for your answer
>
>
>
> I don’t have Amber 14 license, then based on your suggestion, I will use
> AmberTools 14 includes sander. Now, I have 3 questions:
>
>
> 1) Is pmemd needful for sander and md simulation. Can’t I use sander in
> AmberTools 14 without pmemd? Please give me more explanation about the
> importance of pmemd.
>
pmemd gives the same answers as sander and only has a small subset of
sander's functionality (e.g., it does not do QM/MM, EVB, PIMD, LCOD
restraints, chemical shift restraints, NOESY restraints, etc.). But it
runs substantially faster. On CPUs, it's ~2x faster and scales better on
parallel hardware. On GPUs, it's ~10x faster still.
>
> 2) Is there any instruction for installation of AmberTools 14 on CentoS
> 6.3?
>
Installation is the same for basically all distros -- the only thing that
differs is *how* to install the prerequisites. CentOS is in the same
family as Fedora and Red Hat, so follow the fedora instructions here:
http://ambermd.org/ubuntu.html
> 3) Already, I had installed AmberTools 14 Ubuntu 11.04 using this link:
>
> http://bgamari.github.io/posts/2011-10-16-amber.html
>
>
> <http://bgamari.github.io/posts/2011-10-16-amber.html>
>
> you said, sander is included in AmberTools 14. How to use sander in
> AmberTools 14? Using following command?
>
>
> $AMBERHOME/exe/sander -O -i *.in -o *.out -p *.prmtop -c *.inpcrd -r *.rst
>
$AMBERHOME/exe has not existed for many years. It is $AMBERHOME/bin now.
But that general command works.
I suggest going through some of the Tutorials, which will likely help you
get started (especially tutorial B0) at
http://ambermd.org/tutorials/
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 22 2015 - 04:30:03 PDT
