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[[ Category: APBS ]]
[[ Category: APBS FAQs ]]
[[ Category: CCPB workshop ]]

There are many cases where it is inconvenient to run calculations on your own computer:  your calculation may require more resources (memory, etc.) than available on your system, you may have many calculations to run, etc.  
There are two primary mechanisms for running [http://www.poissonboltzmann.org/apbs APBS] on external resources:  the [[#APBS Opal client|APBS Opal client]] and the [[#NBCR Opal web interface|NCBR Opal web interface]].  

== [http://www.poissonboltzmann.org/apbs APBS] Opal client ==
The [http://www.poissonboltzmann.org/apbs APBS] Opal client is a '''drop-in replacement''' for the main [http://www.poissonboltzmann.org/apbs APBS] executable.  As such, it can be used in place of the [http://www.poissonboltzmann.org/apbs APBS] executable ''for any of the examples in this documentation''.<br>

{{ APBS Opal client }}

== [[NBCR]] Opal web interface ==
[http://www.poissonboltzmann.org/apbs APBS] can also be run via the web for users who are uncomfortable with command-line execution or have limited control over installation of new programs on their computer.

In this example, we will perform an [http://www.poissonboltzmann.org/apbs APBS] run using the [http://ws.nbcr.net/opal/GetServicesList.do NBCR Opal service]. The example will use a version of the [http://apbs.svn.sourceforge.net/viewvc/apbs/trunk/examples/born/ Born example] provided with [http://www.poissonboltzmann.org/apbs APBS] modified to produce electrostatic potential output.  The files used are: [[Media:ion-pot.in|ion-pot.in]] (the [http://www.poissonboltzmann.org/apbs APBS] input file) and [[Media:ion.pqr|ion.pqr]] (the structure file).  Please click on the images below for higher-resolution versions of the screenshots for each step.

# Launch the [http://www.poissonboltzmann.org/apbs APBS] [[Opal]] web applications at the [[NBCR]] [[Opal]] Dashboard (http://ws.nbcr.net/opal/GetServicesList.do)<br>[[Image:opal-web-1.png|The Opal Dashboard|200px]]
# Type in the command line instructions [[Running APBS|typically provided]] for an [http://www.poissonboltzmann.org/apbs APBS] command line run (excluding the executable name and path)<br>[[Image:opal-web-2.png|Entering APBS commands|200px]]
# Click on "Choose File" to upload the first file for the [http://www.poissonboltzmann.org/apbs APBS] run.<br>[[Image:opal-web-3.png|Choosing an input file for the APBS Opal web run|200px]]
# Navigate to the file on your local file system and select it.<br>[[Image:opal-web-4.png|Choosing an input file for the APBS Opal web run|200px]]
# The input structure file also needs to be provided. Click on "Add Another File". Navigate to the second file, and select it for upload.<br>[[Image:opal-web-5.png|Choosing a structure file for the APBS Opal web run|200px]]
# Add in any additional files required for the run (for example, if you have additional XML or PQR files specified in your [http://www.poissonboltzmann.org/apbs APBS] input script.<br>[[Image:opal-web-6.png|Choosing additional files for the APBS Opal web run|200px]]
# Once all of the files are uploaded, click the "Submit" button.<br>
# After submission, the [[Opal]] web service will begin refreshing the page to alert you to the status of your run (you do not need to manually refresh the page).<br>[[Image:opal-web-8.png|Waiting for the APBS Opal web run|200px]]
# Once the run is complete the [[Opal]] web service page will update, and the link provided on the page will direct you to your output files.<br>[[Image:opal-web-9.png|Getting results from the APBS Opal web run|200px]]
# Follow the link to download or view the output from your [http://www.poissonboltzmann.org/apbs APBS] [[Opal]] run.<br>[[Image:opal-web-10.png|Getting results from the APBS Opal web run|200px]]