Re: [AMBER] PLUMED patching with AMBER

From: Sanjib Paul <sanjib88paul.gmail.com>
Date: Fri, 13 Nov 2015 17:36:56 +0530

Hii,
      Thank you very much both of you. Initially I was using AmberTools14
along with Amber14. Now I have upgraded AmberTools14 to AmberTools15. Then
I have installed mpi version of sander. I have also successfully installed
PLUMED. During installation of PLUMED I used '--prefix' flag to install it
my own directory not in system directory. Now when I going to run sander
including two extra variables (plumed=1, plumedfile = 'plumed.dat') in
input file I am getting following error message.

*+++ ERROR: you are trying to use plumed, but it is not available +++*
*+++ Check your PLUMED_KERNEL environment variable +++*

From PLUMED website I have come to know that there is a file named '
*modulefile*' in '*$prefix/lib/plumed/src/lib*' by editing which I can set
these environment variables. So I checked 'modulefile and noticed
everything is all right there. What should I do to overcome this problem?
Please help me out.

Thanking you.
Sanjib

On Thu, Nov 12, 2015 at 10:15 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Thu, Nov 12, 2015 at 11:35 AM, Giovanni Bussi <giovanni.bussi.gmail.com
> >
> wrote:
>
> > Jason, you are right.
> >
> > Ambertools 15 comes pre-patched with plumed, with a procedure that is
> > equivalent to doing:
> > plumed patch --runtime -p
> >
> > However, as far as I understood Sanjib is using Amber 14.
> >
>
> ‚ÄčAmber 14 currently runs alongside AmberTools 15. Unfortunately the
> meaning of "Amber 14" is a little ambiguous given the staggered release
> schedule of Amber and AmberTools. I suspect that Sanjib is actually
> running AmberTools 15 alongside a copy of Amber 14.
>
> So if Sanjib *is* using AmberTools 14, the best approach is to use
> "./update_amber --upgrade" to upgrade to AmberTools 15, and then Plumed
> should just work.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 13 2015 - 04:30:03 PST
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