Hello
I have already compiled amber version and its working fine
so I tried to recompile sander with -DLES option
i followed following steps
cd $AMBERHOME/src/sander
make clean
make parallel AMBERBUILDFLAGS=’-DLES’ sander
I got the following error
undefined reference to `EVB_PIMD_INIT.in.EVB_PIMD'
runmd.o(.text+0x9dba): In function `runmd_':
: undefined reference to `EVB_PIMD_DEALLOC.in.EVB_PIMD'
runmd.o(.text+0x10474): In function `runmd_':
: undefined reference to `nose_hoover_init_les__'
thanks
On Tue, Apr 20, 2010 at 3:50 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> sounds like you probably didn't compile properly. we don't know anything
> about how you did that so can't help.
>
> if you pla to upgrade to Amber 11 when it is released in a few weeks, the
> NEB method is completely updated, support larger systems and explicit
> solvent, and is much easier to use. it might be worth waiting if you
> haven't
> already started your NEB project.
>
> On Tue, Apr 20, 2010 at 12:11 AM, jani vinod <genomejani.gmail.com> wrote:
>
> > hello ross,
> > Thanks for reply
> > Sorry, I misinterperated the path intergral dynamics input with NEB and
> > used sander.les.mpi
> > I generated the Input prmtop and inpcrd files for NEB using addles
> > but when I am using sander.MPI the sander get crashed stating
> >
> > Flags: MPI USE_MPI_IN_PLACE
> > *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
> > THAT WERE CREATED BY ADDLES, WITH NPARM=1
> > USE A VERSION COMPILED WITH -DLES
> >
> > And when i am trying to compile sander using -DLES option i am gettin g
> > following error
> >
> > undefined reference to `EVB_PIMD_INIT.in.EVB_PIMD'
> > runmd.o(.text+0x9dba): In function `runmd_':
> > : undefined reference to `EVB_PIMD_DEALLOC.in.EVB_PIMD'
> > runmd.o(.text+0x10474): In function `runmd_':
> > : undefined reference to `nose_hoover_init_les__'
> >
> >
> > thanks
> >
> >
> >
> > On Tue, Apr 20, 2010 at 2:00 AM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> >
> > > Hi Jani,
> > >
> > > > I am trying to run the Nudged Elastic Band Approach tutorial* *with
> > > > amber10.
> > > > In amber10 manual it is giving that their no separate sander.pimd.MPI
> > > > for
> > > > amber10 and one has to use sander.LES.MPI
> > >
> > > Where did you find this in the manual since it is not correct. From
> Page
> > > 134
> > > of the AMBER 10 manual:
> > >
> > > "The NEB capability is implemented inside sander.MPI because of the
> > > similarity between
> > > PIMD and NEB. Input prmtop and inpcrd files for NEB should be generated
> > > using addles"
> > >
> > > You should use sander.MPI (NO LES).
> > >
> > > If you let me know where in the manual it refers to sander.LES.MPI I
> will
> > > make sure a correction is posted.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > >
> > > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not
> > > be read every day, and should not be used for urgent or sensitive
> issues.
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
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> > >
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> >
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Received on Tue Apr 20 2010 - 20:30:03 PDT
