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Output: Water Sphere Log File
- 1
- Output of your water sphere minimization-equilibration simulation will be returned to the 1-2-sphere directory. Go there by typing cd ../1-2-sphere . List the files in the directory by typing ls .
Based on the descriptions in the Output part of the ``Simulation Parameters" section, your present simulation should yield these eleven output files:
- ubq_ws_eq.log
- ubq_ws_eq.coor
- ubq_ws_eq.vel
- ubq_ws_eq.xsc
- ubq_ws_eq.dcd
- ubq_ws_eq.restart.coor
- ubq_ws_eq.restart.vel
- ubq_ws_eq.restart.xsc
- ubq_ws_eq.restart.coor.old
- ubq_ws_eq.restart.vel.old
- ubq_ws_eq.restart.xsc.old
(Your original configuration file should also still be in the directory.)
Seven of the output files contain binary data so that coordinate and velocity information may be kept to high precision. The files which are not in binary code are:
- *
- ubq_ws_eq.xsc, ubq_ws_eq.restart.xsc, ubq_ws_eq.restart.xsc.old, which are extended system configuration files. They store the periodic cell dimensions of the system and the time step at which this information was taken. They are not useful when periodic boundary conditions are not used. (The restart files function in the same way as described before.)
- *
- ubq_ws_eq.log, the log file. It is here that the energy of the various force field interactions is stored. The log file stores a lot of information and it will be examined.
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- The first section of the log file, indicated by the Info tag, contains the parameters used to run the simulation, and other useful information about the system, such as the number of atoms, the type and number of bonds, the total mass, and the total charge.
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- After the first section, information about the minimization of the system is displayed beginning with the line labeled TCL. This line states how long the minimization lasts.
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- After that, the pressure of the system is given. For the present simulation, no pressure output is given because NAMD does not define the pressure for a non-periodic system. For your simulation using periodic boundary conditions, you will see values for the pressure.
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- The next part gives a listing of energies of interaction, first defining which are listed with ETITLE, then listing the actual values in kcal/mol every time step next to ENERGY. (The time step (TS) value is a count of the number of timesteps NAMD has performed and is not in units of time, and the temperature (TEMP) value is in K.)
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- The values listed for INITIAL STEP and GRADIENT TOLERANCE are mathematical parameters corresponding to the numerical search for a minimum in the potential. GRADIENT TOLERANCE will decrease over the course of the minimization and may be used to roughly judge the extent of minimization. See Figure 6.
Figure 6:
Typical minimization output in the log file
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- 7
- After minimization, equilibration data are presented in the log file. See Figure 7. The first lines shown in the figure confirm that NAMD is writing the proper information at the proper time step, which you have specified in the configuration file. The following space is where pressures would normally be written.
Note that since they are not pressures here, this space is used to store the total time step of the simulation. Energies at that time step are then fully reported. In this case, they are output every 100 time steps, as specified in the configuration file.
Figure 7:
Typical equilibration output of the log file
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- The end of the file confirms that the final frame of the simulation is being recorded, and provides computational data which may be used to benchmark your run should you wish to change parameters, run on another computer, etc.
The log file for your simulation of ubiquitin in a water box is quite similar to the one described above with the exception of pressure output, as described. See Appendix F for more information on log files.
Next: Analysis of Water Sphere
Up: Basics of NAMD
Previous: Ubiquitin in Generalized Born
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