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This shows you the differences between two versions of the page.

--- wiki:software [2020/05/12 12:09] – admin
+++ wiki:software [2021/07/29 15:48] (current) – [Available Software] admin
@@ Line 1: / Line 1: @@
 ====== Available Software ======
-The following scientific packages are installed on Keck Center workstations:
+These are some of the scientific packages installed on Keck Center workstations:
 ^ Installed software                             ^ Version       ^ Executable ^
 |[[http://ambermd.org|Amber]]                   | 20            |sander, pmemd, pmemd.cuda |
 |[[http://avogadro.sourceforge.net/|Avogadro]]  | 1.0.3         |avogadro |
-|[[http://www.poissonboltzmann.org/apbs|APBS]]  | 1.5           |apbs |
+|[[http://www.poissonboltzmann.org/apbs|APBS]]  | 3.0.0         |apbs |
-|[[http://browndye.ucsd.edu/|BrownDye]]         | 2018.5.1      |bd_top |
+|[[http://browndye.ucsd.edu/|BrownDye]]         | 2.0           |bd_top |
-|[[http://ivl.calit2.net/wiki/index.php/CalVR|CalVR]]| 2013.12.2 |CalVR |
-|[[http://www.ccdc.cam.ac.uk| Cambridge Structural Database]] | 2014    | cq  |
 |[[http://www.charmm.org|charmm]]               | c41b2         |charmm |
 |[[http://daltonprogram.org/|Dalton]]           | 2016.2        |dalton.x  |
@@ Line 16: / Line 14: @@
 |[[http://www.gaussian.com/|Gaussview]]         | 5.0.9         |gview.exe |
 |[[http://www.gromacs.org/|Gromacs]]            | 5.1.2         |gmx  |
-|[[http://kepler-project.org|Kepler]]           | 2.4           |kepler.sh |
 |[[http://www.mathworks.com/products/matlab/|Matlab]] | 2018a   |matlab |
-|[[http://mgltools.scripps.edu/|mgltools]]      | 1.5.7r1       |pmv |
+|[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2020   |moe |
-|[[http://www.clcbio.com/products/molegro/|MMV]]| 2.5.0         |mmv |
-|[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2019   |moe |
 |[[http://simtk.org/home/msmbuilder|MSMBuilder]]| 2.5           |misc.  |
-|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 2.13          |namd2 |
+|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 3.0           |namd3 |
-|[[http://orcaforum.cec.mpg.de/|ORCA]]          | 4.2.0         |orca |
+|[[http://orcaforum.cec.mpg.de/|ORCA]]          | 5.0.1         |orca |
-|[[http://www.pymol.org|Pymol]]                 | 2.3.0         |pymol |
+|[[http://www.pymol.org|Pymol]]                 | 2.4.0         |pymol |
-|[[http://pyrx.sourceforge.net|PyRx]]           | 0.9           |run.sh |
+|[[https://www.rosettacommons.org/|Rosetta]]    | 3.9           |   |
-|[[https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page|Relion]] | 2.0   |relion |
+|[[http://www.schrodinger.com|Schrodinger]]     | 2021          |maestro |
-|[[https://www.rosettacommons.org/|Rosetta]]    | 3.5           |   |
+|[[http://www.ks.uiuc.edu/Research/vmd|VMD]]    | 1.9.4         |vmd |
-|[[http://www.schrodinger.com|Schrodinger]]     | 2019          |maestro |
-|[[http://vina.scripps.edu/|vina]]              | 1.1.2         |vina |
-|[[http://www.ks.uiuc.edu/Research/vmd|VMD]]    | 1.9.3         |vmd |
 ====== How to use it ======
@@ Line 107: / Line 99: @@
 You can find more information about the modules management [[http://modules.sourceforge.net|package]] on this help [[https://www.nersc.gov/users/software/nersc-user-environment/modules/|page]]. Also here is the module [[http://modules.sourceforge.net/man/module.html|man page]].
 ====== Application specific notes ======
-===== Amber =====
-Before running the CUDA enabled version of pmemd you need to initialize your environment with these two commands:
-<code>
-module load amber/16
-module load cuda/7.5.18
-</code>