PLOT

NAME
PLOT - Write solute coordinates and connection table to a history file in Protein Data Bank Format (PDB).

SYNOPSIS
PLOT  fplot   OPEN  filename
PLOT  FRAGMENT fplot   OPEN  filename
PLOT  ALCHEMY fplot   OPEN  filename
PLOT  CENTER fplot   OPEN  filename
PLOT  STEER fplot   OPEN  filename
PLOT  STEER_ANALYTIC fplot   OPEN  filename
PLOT  STEER_TEMPERATURE fplot   OPEN  filename

DESCRIPTION
It writes a history formatted file containing the coordinates of selected part of the solute (and) the solvent coordinates. The dumping frequency in fs is fplot.

EXAMPLES
PLOT 10.0 OPEN test.pdb
Write coordinates of the backbone atoms of the solute in PDB format every 10 fs to file test.pdb
PLOT CENTER 10.0 OPEN test.pdb
Write coordinates of all atoms of the system in PDB format every 10 fs to file test.pdb. Identical to ASCII_OUTBOX(&INOUT)
PLOT FRAGMENT 10.0 OPEN test.xyz
Write coordinates of a fragment of the solute (in xyz format) selected according the DEF_FRAGMENT (&PROPERTIES) directive every 10 fs to file test.xyz. The fragment is defined as follows:

 
&PROPERTIES 
  ....  
  DEF_FRAGMENT 1 38 
  ...
&END

The file test.xyz can be animated using the XMOL public domain molecular graphics program.

This defines a fragment consisting of the first 38 atoms of the solute. The numeral order of the atoms corresponds to that specified in the topology file (Sec. 10.3).
PLOT STEER 50.0 OPEN wrk.out
write the accumulated work (see Eq. 8.16) to the file wrk.out every 50 fs. The accumulated work at time $t$ is calculated as ${\cal W} = {\cal H}(t) -{\cal H}(0)$, where ${\cal H}(t)$ is the total energy of the microcanonical extended system, i.e. it includes the energy of the thermostat and/or of the barostat. If the integration time steps are too large and the simulation shows a energy drift, then the accumulated work includes the dissipation due to the energy drift of the integrator.
PLOT STEER_ANALYTIC 50.0 OPEN WRK.out
Write the accumulated work (see Eq. 8.16) to the file wrk.out every 50 fs. The accumulated work at time $t$ is calculated analitically according to Eq. 8.16. This option is slightly more computationally demanding than the previous one, but in this case, the accumulated work is not affected by the energy drift. The last two commands are to be used in conjunction with the STEER(&RUN) command and with the commands ADD_STR_BONDS, ADD_STR_BENDS, ADD_STR_TORS (namelist &POTENTIAL) for defining an external steering potential for SMD.
PLOT STEER_TEMPERATURE 50.0 OPEN WRKTEMP.out
In a steered temperature simulation[150], write the accumulated (adimensional) thermal work every 50 fs to the file WRKTEMP.out. This command must be used in conjunction with the STEER (&RUN) command for steered molecular dynamics simulations and with the THERMOS(&SIMULATION) command for running NVT simulations.
PLOT ALCHEMY 50.0 OPEN alchemic.wrk
Print to the file alchemic.wrk the work done during an alchemical transformation. See also commands DEFINE_ALCHEMICAL_ATOM and STEER ALCHEMY.