Re: [AMBER] PLUMED patching with AMBER

From: Sanjib Paul <sanjib88paul.gmail.com>
Date: Sat, 14 Nov 2015 18:27:51 +0530

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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Nov 14 2015 - 05:00:02 PST
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