AMBER Archive (2006)

Subject: AMBER: Problem with file size of sander outputs

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Feb 22 2006 - 01:54:24 CST

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_at_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_at_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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