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Pair interaction calculations

NAMD supportes the calculation of interaction energy calculations between two groups of atoms. When enabled, pair interaction information will be calculated and printed in the standard output file on its own line at the same frequency as energy output. The format of the line is PAIR INTERACTION: STEP: step VDW_FORCE: fx fy fz ELECT_FORCE: fx fy fz. The displayed force is the force on atoms in group 1 and is units of kcal/mol/Å.

For trajectory analysis the recommended way to use this set of options is to use the NAMD Tcl scripting interface as described in Sec. 2.2.2 to run for 0 steps, so that NAMD prints the energy without performing any dynamics.


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Next: Pressure profile calculations Up: Runtime Analysis Previous: Runtime Analysis   Contents   Index
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