The NAMD molecular parallel molecular dynamics package is supported from the University of Illinois NCSA as part of the NIH bioinformatics software effort. It scales to use some dozens of processors using gigabit ethernet. It uses VMD for simulation setup, but is also file-compatible with AMBER, CHARMM and X-PLOR.
To load NAMD, type
source /usr/local/apps/NAMD/namd210.cshIf the file bnamd2 is in the same directory as the input file energies.conf, then executing the command
bsub < bnamd2
#!/bin/csh #BSUB -o o.%J #BSUB -e e.%J #BSUB -W 15 #BSUB -R span[ptile=4] #BSUB -n 4 source /usr/local/apps/NAMD/namd210.csh mpirun namd2 ubq_wb_eq.conf > ubq_wb_eq.log
A few sample runs can be found in /home/gwhowell/apps/samples/namd-tutorial-files.
cd /home/gwhowell/apps/samples tar cvf pathyouwanttoputthetarfile/namd-tutorial-files.tar namd-tutorial-files cd pathyouwanttoputhetarfile tar xvf namd-tutorial-files.tar cd namd-tutorial-filesIn the directory 2-3-energies there are some sample "btry" files which successfully run namd in some sample cases. The user need only change the paths for the -o and -e standard output and error.
Last modified: September 30 2020 18:08:01.