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Subsections


NAMD configuration parameters

Input files

Output files

Standard output

NAMD logs a variety of summary information to standard output. The standard units used by NAMD are Angstroms for length, kcal/mol for energy, Kelvin for temperature, and bar for pressure. Wallclock or CPU times are given in seconds unless otherwise noted.

BOUNDARY energy is from spherical boundary conditions and harmonic restraints, while MISC energy is from external electric fields and various steering forces. TOTAL is the sum of the various potential energies, and the KINETIC energy. TOTAL2 uses a slightly different kinetic energy that is better conserved during equilibration in a constant energy ensemble. Although TOTAL2 is calculated internally for producing TOTAL3, its value is no longer output during simulation. TOTAL3 is another variation with much smaller short-time fluctuations that is also adjusted to have the same running average as TOTAL2. Defects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2.

PRESSURE is the pressure calculated based on individual atoms, while GPRESSURE incorporates hydrogen atoms into the heavier atoms to which they are bonded, producing smaller fluctuations. The TEMPAVG, PRESSAVG, and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output; for the first step in the simulation they will be identical to TEMP, PRESSURE, and GPRESSURE.

Performance for NAMD's new GPU-resident mode is improved by avoiding calculation of energy and virial reductions except when needed. This means that the averages are no longer calculated over all values since the previous ENERGY output. Instead, a moving average is calculated over the previously output values, using a fixed window size defined by a config file parameter. GPU-resident mode replaces TOTAL3 with TOTALAVG, a moving average over the previous TOTAL energy values.

Output Selection

For the cases when it is preferable to have trajectory output of a subset of the atoms, selections can be defined and assigned independent output frequencies and output file names.

Atom selections are defined by creating a PDB file where the temperaturefactor field (AKA beta in VMD) is assigned a value greater than zero for each atom in the selection. For example, when the objective is to have a more frequent output trajectory containing no solvent, the following VMD commands will produce an appropriate selection PDB.

(Note: example assumes structure and coordinates are already loaded)

set allatoms [atomselect top "all"]
set soluteatoms [atomselect top "not water and not ions"]
$allatoms set beta 0
$soluteatoms set beta 1
$allatoms writepdb solute.pdb
$soluteatoms writepsf solute.psf

The additional PSF file in the prior example is not necessary for NAMD, but would be useful in VMD, or other subsequent analysis, to examine the trajectory associated with given selection of atoms.

Such selections can be used within NAMD using the arguments described below. A maximum of $ 16$ such selections is allowed. There are no restrictions regarding atoms belonging to multiple selections. Each selection is identified by a user defined string tag to bind the frequency and input file and output file definitions together for each selection. The tag is an alphanumeric string without spaces, up to $ 80$ characters in length, which identifies to which selection the specified field applies.

In the case of the example above, the following configuration would be valid:

dcdSelection yes
dcdSelectionInputfile soluteonly solute.pdb
dcdSelectionfreq soluteonly 100
dcdSelectionfile soluteonly solute.dcd

NOTE: This feature is not currently compatible with special memory-optimized NAMD builds https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction.

See lib/replica/examples/mplexjob0-dcdselect.conf for replica usage.


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Next: AMBER file and force Up: Input and Output Files Previous: File formats   Contents   Index
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