Resources

Titlesort ascending Body File Updated date Author
Updated NMW scripts

  • These scripts were developed to mirror the previous NMW scripts.

     

    converterCAOnly- will only take the C-alpha vectors. This will make VMD easily display a readable amount of information.

     

    converterDipole- Will create a single atom at the position zero with the Dipole Derivative vector.

     

    converterFull- Mirror of previous script, but with a fix for .pdb files with over 1000 atoms.

     

     
Tuesday, October 25, 2016 - 00:34 Ryan Nyweide
SS1010 motor controller & Howard 1-19-4100 stepper motor

  • We ran into issues wiring our stepper motor to this motor controller, which was made worse by the lack of documentation on the motor itself. This PDF has a link to more information on the motor as well as how we wired it to our controller board in order to get it to operate correctly.
Tuesday, July 7, 2015 - 11:30 Nigel Michki
Optics Workbench:

  • Rendered originally in autocad inventor by Akansha Sharma.

    Below is the link to the page of Optics Workbench.                                                                                                                                                                                                                                                                                                                        http://markelz.physics.buffalo.edu/optics-workbench

     

     

     

     

 Tuesday, June 6, 2017 - 15:47 Prof. Andrea Markelz
Nigel Michki's Most Excellent Script for using NMWiz

  • NMWiz is an awesome add in for VMD for quickly visualizing and animating modes.  However the expected input files are from the Bahar group's ProDy program.  Nigel Michki put together an excellent python script that converts charmm normal mode analysis output to the required format for NMWiz.  We love it!  Note because it is all atom, the animation is too slow, but the vector visualization is very useful.  We hope to make a new script to reduce the vectors to just C-alphas.  You will need to remove the .txt ending.  This was appended by drupal.  
Monday, November 2, 2015 - 10:08 Prof. Andrea Markelz
Lot's o' force field tutorial links
Monday, November 2, 2015 - 10:19 Prof. Andrea Markelz
Binary compatibility issues

  • From: http://pelican.rsvs.ulaval.ca/mediawiki/index.php/CHARMM_tips_and_tricks

    If you encounter the message "Headers do not match", it may be caused by :

    §  Using a different machine type (x86 vs AMD64)

    §  Using a different compilation of CHARMM

    Here is the solution :

    From the machine which generate the (binary) trajectory file :

        open unit 10 unform name merge.trj    open unit 20   form name form_merge.trj    DYNA FORM FIRST 10 OUTP 20

    From the machine which will read this formatted trajectory

     

        open unit 10   form name form_merge.trj    open unit 20 unform name merge.trj    DYNA UNFO INPUT 10 OUTP 20
 Thursday, November 5, 2015 - 11:17 Prof. Andrea Markelz