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SOMD MD tutorial ####Step Three: Production Run The production run of a simple MD simulation is pretty straight forward and can again be done using a similar config script to the equilibration ones. Let us first create a directory for the production run and copy the last frame of the npt simulation into that directory. Let’s start again in the top directory of the tutorial, where ls gives the following output Equib FESetup

mkdir Production
cd Production
cp ../Equib/1AKI.parm7 .
~/sire.app/bin/ipython 
import mdtraj as md
t = md.load('../Equib/npt/traj000000001.dcd', top='1AKI.parm7') #loading trajectory and topology. 
t[-1].save('npt.rst7')
exit

This prod.cfg [file] (Data/prod) is an example file that will run 1 ns of unrestrained dynamics of Lysozyme. It can again be executed in the following way:

somd -C prod.cfg

On my workstation using the CUDA platform and a GTX980 the simulation takes about 800 s.

Let’s have a look at some of the config file features that can be used for simulations. You can for example specify the platform on the command line when submitting a somd job, e.g.

somd -C myconf.cfg -d 1 -p CUDA

Would mean that you select device 1 using the CUDA platform. For Nvidia devices you can check your device ID, by for example running:

nvidia-smi

+------------------------------------------------------+                       
| NVIDIA-SMI 352.21     Driver Version: 352.21         |                       
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla C2075         Off  | 0000:03:00.0      On |                    0 |
| 30%   80C   P12     0W / 225W |    120MiB /  5375MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
|   1  GeForce GTX 980 Ti  Off  | 0000:04:00.0     Off |                  N/A |
| 47%   81C    P2    81W / 250W |    138MiB /  6143MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    1      4217    C   /home/username/sire.app/bin/somd           117MiB |
+-----------------------------------------------------------------------------+

All configuration file options for a somd run can be displayed by simply typing:

somd -H

Take any of the parameters and copy it into the config file of your simulations to play around with. Most options should be relatively self explanatory. Some of the options may not apply to the simulation you are trying to run and good care has been taken to select sensible default options, allowing for using minimal config files.

####Restarts If you simply want to extend an existing simulation execute the same somd command from before (e.g. somd -C prod.cfg) and the simulation will continue from the simulation state saved in the sim_restart.s3 file. However, a new trajectory will be written, so that you do not have to worry about overwriting trajectories. Sire will automatically look for a restart file. Should you wish to run a completely new simulation, you will either have to remove the *.s3 files in the directory where you want to run your simulation or create a new directory for a fresh simulation.