[Chimera-users] Sending Chimera MD job to remote computer

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 14 14:28:33 PDT 2021

Hi Connor,
	The MD simulation provided by Chimera is intended for short-ish simulations on small-ish systems, where you would get results in a matter of minutes and be able to view them in the same session of Chimera.  If you want to run simulations that are big enough or long enough that you need bigger servers, I would strongly recommend using dedicated MD packages such as Amber, CHARMm, Gromacs, or NAMD.  Their code is fine tuned for maximum performance and will be able to complete computations significantly faster than Chimera's MD code can.  The MD code provided by Chimera can only run MD in the Chimera process.
	That said, there is disabled and untested code in the MD module to run MD as a separate process.  If you are Python savvy you could change some things in the <Chimera app>/share/md module to enable it.  In the dynamics() routine in mdMMTKinter.py file, you would change the first 'if' statement to always call self.runInBackground(...).  Then you would change that routine to not actually start the background job but instead print out the location of the MMTK universe (.mmtk extension) and Python script (.py extension) files that it wrote.  You would have to move them to the server machine and run them in "nogui" mode (<Chimera app>/bin/chimera --nogui python-script).  I have absolutely no idea if this would work.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jun 13, 2021, at 11:16 AM, Cowie, Connor via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username at detroit05 (and then entering the password). However, I want to be able to send a command to a remote computer to improve the computational time especially when running multiple MD simulations; right now, I am running MD simulations on the same computer. I was first thinking of a sequence of commands below:
> Ctrl+Z
> bg
> ssh -y username at detroit05
> I know that the Ctrl+Z command temporarily pauses a command, but I believe that the jobs command is first needed to list the current running jobs (that Ctrl+Z can be performed on). However, the running jobs are not listed when I type “jobs”. After using the “top” command to list all of the processes, I have verified that the Kill command works by typing these in succession:
> Kill -STOP PID#
> Kill -CONT PID#
> Can you walk me through how to first have a listing of jobs running in Chimera and then sending it to a remote computer?
> Best,
> Connor
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