142. MD = Ecce + NWChem. 3. Energy

Update 19 June 2013:
A much better written and complete guide to getting started with MD in ECCE+NWChem is found here: http://saccharides.blogspot.tw/2013/06/ecce-md-calculation.html

Original post:

Part 1:
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-1-prepare.html

Part 2:
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-2-md-optimize.html

Part 4.
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-4dynamics.html

Rightclick and select new, Energy

 Double-click on the new icon

 Click on editor

 Set up your calc, then launch

It should run quickly. There's little to see in terms of output except for single-point energies.

141. MD = Ecce + NWChem. 2. MD Optimize

Update 19 June 2013:
A much better written and complete guide to getting started with MD in ECCE+NWChem is found here: http://saccharides.blogspot.tw/2013/06/ecce-md-calculation.html

Original post:

Part 1 is here: http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-1-prepare.html

Part 3:
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-3-energy.html


Part 4.
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-4dynamics.html

Rightclick on your project and select create new, Optimeze

Double-click on the icon that was created

 Click on editor

You can now configure the optimization.

 Things you may want to look at are the number of steps

 and whether you use SHAKE or not -- 100% of failed attempts so far have been related to SHAKE.

Launch. This will take longer than the Prepare step. A lot longer.

Displaying the result might also take a while -- here's a 2x2x2 box with 100 iterations:
without showing solvent

showing solvent

140. MD = ECCE + NWChem: 1. Prepare

Update 19 June 2013:
A much better written and complete guide to getting started with MD in ECCE+NWChem is found here: http://saccharides.blogspot.tw/2013/06/ecce-md-calculation.html

Original post:
Here's a multi-part description of how to set up a minimal MD simulation using ECCE/NWChem. To make things real easy we'll do an example with a fully described and parametrised system.

Part 2:
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-2-md-optimize.html

Part 3:
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-3-energy.html

Part 4:
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-4dynamics.html


How to install and configure ecce is described elsewhere on this blog.

Start here
Start Ecce, select Organizer

 Rightclick in the organiser and create a new MD Study

 Rightclick on the new project, and create a MD Prepare

 This is what you should have now. Double click on the Prepare icon, then click on the Editor icon

 You get this menu. Click on the Builder icon in the bottom left corner.

Click on the Import from Structure Library icon (hidden behind the dropped down menu in the screenshot). Go to RNA bases, monomers and select Cytidine. Also, check the Atom table and Coordinates options in the Tools menu.

 Hit ctrl+s to save, and close the window.

Back in the organiser set the size of the box for the system

 And click on solvate. You'll see what commands are being added to your input files.

 You might not be able to launch at this point, with ecce complaining about being unable to find the pdb. For me, opening the builder and clicking on Center in the Coordinates box on the right (make it show by checking the right box in Tools menu in the Builder)

If all goes well you'll be able to launch your job, which will finish very fast.

 And here's what we have at this point.

Part 2 will do the next step -- MD Optimize