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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Received on Mon Apr 19 2010 - 21:30:03 PDT
