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noviembre, 2015:

AMBER

General information

14 version of AMBER (Assisted Model Building with Energy Refinement) and AMBER-tools15. Program with empiric potentials with molecular dynamics and energy minimization. Especially oriented to the simulation of biological systems.

How to use

The serial and parallel version have been compiled and can be found in the direktory

/software/bin/amber/

send_amber

To send jobs to the queue system you can use the send_amber command:

send_amber "Sander_options" Nodes Procs_Per_Node[property] Time [or Queue] [Mem]  ["Other_queue_options"]

Sander_options: the options you want to use in the calculation, inside quotes
Nodes: is the number of nodes
Procs: is the number of processors (you may uinclude the node type) per node.
Time: or Queue the walltime (in hh:mm:ss format) or the queue name of the calculation
Mem: the PBS memory (in gb)
[Mem] and ["Other_queue_options"] are optional

For “Other queue options” see examples below:

send_amber "sander.MPI -O -i in.md -c crd.md.23 -o file.out" job1 1 8 p_slow
send_amber "sander.MPI -O -i in.md -c crd.md.23 -o file.out" 2 8:xeon vfast 16 "-W depend=afterany:1234"
send_amber "sander.MPI -O -i in.md -c crd.md.23 -o file.out" 4 8 24:00:00 32 "-m be -M mi.email@ehu.es"

More information

Amber home page.

On-line manual.

Tutorials.