Try to divide your calculation into different output files restarting them
with NTX=5, and IREST=1...
Good look
G.
At 11:54 p.m. 21/02/2006 -0800, you wrote:
>Dear amber community,
>
>I have been running a PME explicit solvent molecular
>dynamics for a 20 KDa protein and its ligand using the
>sander module of AMBER8.
>I set nstlim=40000 and ntpr=10. After a couple of
>hours , my MD run stopped at nstep =9970 giving me the
>following error message:
>
>Filesize limit exceeded
>
>My trajectory file size has reached to 2 GB, the MD
>output is 666 Kb and the coordinate output is 6.6 MB.
>
>I believe I will have to recompile sander changing
>some codes to increase the file size in sander. Could
>someone please let me know what codes in sander should
>be modified?
>
>cheers,
>
>jenk.
>
>
>
>
>
>
>--- Ross Walker <ross.rosswalker.co.uk> wrote:
>
> >
> > > ./configure -mpi ifort
> > > make parallel
> >
> > -mpi means native MPI libraries as provided by the
> > operating system. This is
> > the option to use for things like an SGI altix. For
> > a regular PC running
> > redhat you need to provide an mpi installation
> > either MPICH or LAM. This MPI
> > installation needs to be compiled with the same
> > compiler as you are using
> > for compiling Amber. Hence the lam that is often
> > installed by default with
> > redhat will not work as it is compiled with GCC.
> >
> > So, download either Lam or MPICH, compile it with
> > ifort and chech your PATH
> > is correct so that the correct installation is being
> > used.
> >
> > E.g. which lamboot
> >
> > should return /usr/local/lam/lamboot (or similar)
> > rather than /usr/bin/lamboot
> >
> > Once this is done create a config.h for the lam or
> > mpich:
> >
> > export LAM_HOME=/usr/local/lam..... (or where you
> > installed it)
> > ./configure -p4 -lam ifort
> > or
> > export MPICH_HOME=/usr/local/mpich.....
> > ./configure -p4 -mpich ifort
> >
> > Then:
> >
> > make clean
> > make parallel
> >
> > You should then not get the undefined references you
> > are seeing.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel: +1 858 784 8889 | EMail:-
> > ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on
> > request |
> >
> > 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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Received on Sun Feb 26 2006 - 06:10:13 PST
