Dates and Times of Workshop

Tuesday 22nd February 2pm - 4pm

Monday 28th February 2pm - 4pm

Tuesday 1st March 2pm - 4pm

Monday 7th March 2pm - 4pm

Tuesday 8th March 2pm - 4pm

Overview

Use of NAMD (a general purpose MD package designed to work on both single stand-alone computers and parallel clusters).

Exercises

Please remember: do not run NAMD jobs on godzilla. You must always submit these to the dedicated queue for the module. Every time you need to type the namd2 command you need to put the entire command line into a job.pbs script and submit the job using qsub (see Workshop Part 1)

Download the NAMD tutorial instructions (lin/mac).

To run the tutorial log into the CSC using the NX client and download the NAMD tutorial files used in the tutorial.

To unzip the tutorial files type

tar -xvf namd-tutorial-files.tar.gz

Remember that in order to use VMD on the CSC machines you need to load the VMD module

module load vmd

And in order to use NAMD on the CSC machines you need to load the NAMD module

 module load namd

   

Assessment

The assessment for the workshops is described at this link.