Running a simple MC simulation

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(please see click for Yang lab website)

Connecting to HPCC

A simple command from your local Cygwin (or Mac) terminal will let you connect to HPCC,

 ssh -l yourCaseID

Or, if X11 is desired, you can try

 ssh -X -l yourCaseID
When prompted,
<use the same password associated with your case ID>

By now, you are not working on your own laptop any more, but a remote computer (or a cluster of computers). In this case, the frontend of this computer cluster has a hostname called Once you are logged in, we can do a lot of things from now on.

This should work if you are using the campus CaseWireless wireless network. However, if you login from off-campus or from the campus CaseGuest wireless network, a VPN client may be required from CWRU.

All the UNIX/Linux commands are available. For example, you can try


showing the current working directory. Or


showing all current running processes, including which Unix shell that is running.

Get your own computer node to play with

Generally, it is a good idea to run computing jobs at the login-node simply because it can slow down the entire cluster system. So, it is recommended to get yourself on one of so-called computing nodes by

   qsub -I

If a large amount of resource, say a large memory node, is required, you can get via

  qsub -I -l mem=8gb

Now you are transferred from the login node to a computing node. You can find out which node you are at by


Some basic of MATLAB

A lot of good examples can be found at the MATLAB website. It has both a graphic and non-graphic/text interface. For this example, we are going to use the text mode by

   matlab -nodisplay

Some simple uses are like:

   a = [1 2];
   b = [3 4]
   c = a + b

A realistic MC code for a two-state conformational change

We are going through this example when we meet. There are three/four files we will use. You can copy them to your own folder (at your current dir) by

  cp -r /home/sxy227/class2015/bmc . 

Now, let us take a closer look ...