Re: [AMBER] PLUMED patching with AMBER

From: Sanjib Paul <sanjib88paul.gmail.com>
Date: Mon, 16 Nov 2015 11:32:25 +0530

Hello Giovanni,
                    Thank you very much. Now it is running properly.

Sanjib

On Sat, Nov 14, 2015 at 10:18 PM, Giovanni Bussi <giovanni.bussi.gmail.com>
wrote:

> You should set it in your shell before running amber eg:
>
> export PLUMED_KERNEL=/path
>
>
>
> Inviato da iPhone
>
> > Il giorno 14/nov/2015, alle ore 13:57, Sanjib Paul <
> sanjib88paul.gmail.com> ha scritto:
> >
> > Hello Giovanni,
> > Environment variable PLUMED_KERNEL is properly set
> in
> > that file. I have checked that. I am sending you that file. Do I have to
> > set this path anywhere else?
> >
> > Thanking you.
> >
> > Sanjib
> >
> > On Fri, Nov 13, 2015 at 8:48 PM, Giovanni Bussi <
> giovanni.bussi.gmail.com>
> > wrote:
> >
> >> 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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> > <modulefile>
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Received on Sun Nov 15 2015 - 22:30:03 PST
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