Testing NAMD

There are sample configuration files in the sample/ directory. After building NAMD, change to the sample/ directory and invoke NAMD on each of the configuration files. (Don't forget to start PVM first!) Assuming that the NAMD executable is in your path, perform the first test by typing:

> namd alanin1.config

The last output line of energies should be approximately:

Info> ETITLE:     TS    BOND        ANGLE       DIHED       IMPRP       ELECT   
    VDW       KINETIC       TOTAL      TEMP       |P|        |L|
Info> ENERGY:   1000 1.7517      8.8425      1.0274      2.4743      -207.3765  
 -29.9398    15.0133     -208.2070  77.4878    4.3095e-14 2.1252e-03

Then perform the second test by typing:

> namd alanin2.config

The last output line of energies should be approximately:

Info> ETITLE:     TS    BOND        ANGLE       DIHED       IMPRP       ELECT   
    VDW       KINETIC       TOTAL      TEMP       |P|        |L|
Info> ENERGY:    100 0.2072      4.7894      0.8302      3.5955      -272.3828  
 -30.9772    13.9564     -279.9814  72.0327    7.6971e-02 6.4902e-01

Note that using FMA on only 66 atoms is expected to be substantially slower than computing full electrostatics using the direct $\mathcal{O}(N^2)$ approach.