Re: [AMBER] PLUMED patching with AMBER

From: Giovanni Bussi <giovanni.bussi.gmail.com>
Date: Fri, 13 Nov 2015 16:18:13 +0100

Look for a file named libplumedKernel.so and set the env var PLUMED_KERNEL
to the full path of that file

Giovanni

On Fri, Nov 13, 2015 at 1:06 PM, Sanjib Paul <sanjib88paul.gmail.com> wrote:

> 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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>
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Received on Fri Nov 13 2015 - 07:30:06 PST
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