Pre-recorded Script Lesson, Output File

This example file has been formatted to aid reading it and contains links giving you access to additional information. Added comments that were not part of the original file are in italics. 

	DISCOVER Molecular Simulation Program

		Version:   95.0 Beta
		Build:     950316
		Date:      Fri Mar 17 11:18:58 1995
		User Name: marj
		Host Name: iris90
		Host Type: iris


----------------------------------------------------------------
Licensed by BIOSYM Technologies to 
BIOSYM SAN DIEGO
----------------------------------------------------------------


NLS: License for Discover_Pgm Checked Out

randomSeed is set to 467941
The randomSeed variable would have to be set to the same number if you wanted to repeat a run exactly. 

Line  12:BTCL> begin
Lines from the input file are printed in the output file, so that you have a permanent record of the calculation conditions. 

INPUT FILES
___________

File Type		Name
---------		----

Forcefield		/ax10/bioroot/develop/release950/irix5r4/biosym_lib/cvff.xfrc
Molecular data		DIFFUSION1.mdf
Coordinate		DIFFUSION1.car
The above were the default forcefield and molecule-specification files.

The collection of water molecules is a periodic system: 

Periodic Boundary Conditions
____________________________

		Length (A)		Angle (degrees)
		----------		---------------

		a 18.62000		alpha  90.00000
		b 18.62000		beta   90.00000
		c 18.62000		gamma  90.00000
Here, the pre-coded BTCL script is sourced: 

Line  15:BTCL> source diffusion.inp

MOLECULAR TOPOLOGY
__________________

Number of molecules:		   216
Number of residues:		   216
Number of atoms:		   648 (asymmetric unit: 648)
Number of atom types:		     2
Number of bonds:		   432
Number of angles:		   216

FORCEFIELD OPTIONS
__________________

Filename		  : cvff.frc
Definition name		  : cvff_nocross_nomorse
Version			  : 2.3
Last modification date	  : 7/29/93
# of automatic parameters : 0

NONBOND ENERGY CUTOFFS
______________________

		Cutoff (A)	Spline Width (A)	Buffer Width (A)

vdW		  9.50		     1.00		     0.50
Coulomb		  9.50		     1.00		     0.50

Summation method for vdW	: Group based
Summation method for Coulomb	: Group based
Dielectric			: 1.00

MOLECULAR DYNAMICS
__________________

Ensemble           :       NVE

Timestep           :      0.25 fs
Duration           :    100.00 fs
Integration Method : Velocity Verlet

Initial Velocities :   Random Velocities from Boltzmann distribution
Initial Temp.      :    298.00 K


Dynamics Summary
________________

			    Initial        Final      Average    Std. Dev. 
			    -------        -----      -------    ---------  

Tot. energy (kcal/mol)    -1313.954     -602.372     -602.388        0.291
Pot. energy (kcal/mol)    -1888.400    -1563.608    -1613.483       55.540
Kin. energy (kcal/mol)      574.446      961.236     1011.095       55.343
Temperature (K)             298.000      498.651      524.516       28.710
Pressure (GPa)             0.189702     1.563395     0.778632     0.503895
Volume (A^3)               6455.636     6455.636     6455.636        0.000
Density (gm/cm^3)            1.0009       1.0009       1.0009       0.0000

Time used by 400 steps is 0 hours 5 mins 30.21 secs (0.826 secs per step)


Total time used by DISCOVER: 5 mins 37.02 secs (337.02 secs)

Completion date: Fri Mar 17 11:28:12 1995
Exiting Discover: status OK.
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