Registration Guide Register for HPC Access to HPCNew User Guide How to Run Batch Jobs Portal User Guide About the Service Subscribe to Pay-Per-Use Service Subscribe to Condominium Service Terms and ConditionsUser GuideHigh Performance Workspace Service Utility Storage ServiceResearch Data Management ServiceCentre for Computational Science & Engineering
 |
||
| Need help? | ||
|
||
 |
||
Amber is a collective name for a suite of program that allow users to carry out and analyze molecular dynamics simulations, particular for proteins, nucleic acids and carbohydrates. It's also a family of force field for molecular dynamics of biomolecules. The Amber9, which is distributed by UCSF subject to a licensing agreement, is available now on atlas2 and atlas3 cluster.
The parallel Sander molecular dynamics jobs can be submitted to the atlas2 and atlas3 Linux cluster through queues linux64_parallel and mcore_parallel by using the following command:
bsub < run_amber9
Example of the content of file run_amber9 is:
#!/bin/sh
#BSUB -o my_amber9_job.eo
#BSUB -q mcore_parallel (or -q linux64_parallel)
#BSUB -n 4 (note: 4 ≤ n ≤ 32 )
#BSUB -a mvapich
mpirun.lsf /app1/linux/amber9/exe/sander.MPI -O -i test.in -p apo.prmtop -c apo.inpcrd -o test.out -r test.rst -ref apo.rst -x test.mdcrd -inf test.info
Jobs can be submitted either from /lsftmp or /svutmp. It's recommended to submit your jobs from the parallel file system /svutmp, as it is parallel file system and a better performance can be achieved from there.
The main preparation programs antechamber and LEaP ( tLEap and xLEap), and the analysis program ptraj is available from the MobileVisLab. Just issue these commands: anterhamber, tleap, xleap or ptraj at the command prompt to start the programs.
