On Mon, Nov 22, 2010 at 10:25 PM, setyanto md <stwahyudi.md.gmail.com>wrote:
> Dear YT
>
> Have you try sander_openMM ? Do you have any problem when install it ?
>
> I've been try, I follow instruction in readme.txt file, They said :
>
> "6) From the directory containing this README.txt file, run the
> addOpenmmToSander.sh Bash script to copy the new source and make files
> to the AMBER source area.
> $ /bin/bash addOpenmmToSander.sh
>
> 7) Change to the AMBER source directory and rerun the make command:
> $ cd $AMBERHOME/src
> $ make clean
> $ make serial
> =================
>
> I've error when make serial.
> The error said : "cannot find -lOpenMM
>
Some familiarity with the process of compiling code would certainly be a
great help here. This error means that a library can't be found.
Specifically, libOpenMM.a (or libOpenMM.so/libOpenMM.dylib depending on your
system/compiling options) in the searched library paths. What you have to
do is locate this library (wherever you installed it), and provide its
location to the linker (-L/path/to/library -lOpenMM). (The fortran compiler
doubles as the linker in the sander build)
It's difficult for me to help beyond this, since I've never used OpenMM.
Hope this helps,
Jason
> But actually i've been install OpenMM.
>
> Can you do me a favor ? please ?
>
> regards
> Setyanto
>
> On Tue, Oct 26, 2010 at 12:59 PM, c00jsw00 <c00jsw00.nchc.org.tw> wrote:
>
> > Hi,
> > The openMM can do it. (https://simtk.org/home/openmm)
> > YT
> > On Mon, 25 Oct 2010 22:38:37 -0700, "Ross Walker" <ross.rosswalker.co.uk
> >
> > wrote:
> > > Dear Setyanto,
> > >
> > >> We have amber 10 in our laboratory. With GPU computing technology, we
> > >> would
> > >> like to know if it is possibly to run Sander on GPU ?
> > >> If yes, could some body help us, how to do it ?
> > >
> > > You cannot currently run sander on GPUs. However AMBER 11 supports use
> > of
> > > GPUs (NVIDIA SM1.3/2.0 and later) for acceleration of pmemd runs.
> > >
> > > See: http://ambermd.org/gpus/
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > ---------------------------------------------------------
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Adjunct Assistant Professor |
> > > | Dept. of Chemistry and Biochemistry |
> > > | University of California San Diego |
> > > | NVIDIA Fellow |
> > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > ---------------------------------------------------------
> > >
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> > not
> > > be read every day, and should not be used for urgent or sensitive
> > issues.
> > >
> > >
> > >
> > >
> > >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Nov 23 2010 - 06:00:04 PST
