Discover Minimization Output File (with convergence)
DISCOVER Molecular Simulation Program, Version 2.97
Date: 03-Jan-99 Time: 17:25:58
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*Line 1 ! INPUT FILE FOR DISCOVER GENERATED BY INSIGHT *
*Line 2 ! *
*Line 3 ! *
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*Line 4 overlap = 0.01 *
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*Line 5 begin simulation *
*Line 6 * add-automatic bond torsion valence out-of-plane *
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Force Field parameters will be selected from the force field library.
The Binary Force Field used is :
/usr/local/msi/950/irix5r4/biosym_lib/cvff.bin
The Binary File was generated from a text file containing the following version information:
cvff.frc 2.3 29-Jul-93
FORCE FIELD INPUT OPTIONS
=========================
potential data options
default updated
cutoff 0.10E+33 0.10E+33 non-bond neighbor list - all residues within cutoff distance are included
cutdis 0.10E+33 0.10E+33 non-bond energy cutoff distance - interactions greater than this are neglected
swtdis 0.00E+00 0.00E+00 switch distance the distance over which the switching function reduces the non-bond energy to zero
Cross term energies will be included.
A morse potential will be used for bond energies.
non-bond switching function: lower bound 0.100000E+07 upper bound 0.100000E+07
coordinate file title: input file for discover 0.0000000E+00
---------------------- !DATE Sun Jan 3 17:25:57 1999
for molecule 1 no. of residues read= 3 no. of atoms read 49
residue names:
LYSn 1 ALA 2 GLUN 3
END OF INPUT: no. of molecules read 1
total no. atoms 49 limit 25000
total no. groups 15 limit 8000
total no. residues 3 limit 7520
total no. molecules 1 limit 7500
total no. bonds 48 limit 30000
total no. valence angles 85 limit 50000
total no. torsion angles 121 limit 75000
total no. out of planes 6 limit 7500
total no. theta*theta angles 144 limit 87500
total no. excluded atoms 508 limit 325000
The following protocol will be used for parameter assignments:
|---------------------------------------------------------------------------|
| type non-automatically 1st non-automatically automatically |
| only then automatically only |
|---------------------------------------------------------------------------|
| |
| bond STOP |
| valence STOP |
| torsion STOP |
| out-of-plane STOP |
| cross-term CONT |
|---------------------------------------------------------------------------|
| If "STOP" is specified, the program will stop when parameters for an |
| internal are not found in the library. If "CONT" is specified, the |
| program will select a value of zero for the parameter and continue. |
|---------------------------------------------------------------------------|
The following table summarizes the number of interactions for which parameters
were either found explicitly in the force field file, automatically generated
from bond order information, or set to zero if not available. Each of the major
classes of interactions is reported separately. A detailed listing of all the
interactions requiring automatically generated parameters has been printed in a
separate file. The default name of the file is "fname".prm (logical unit 1).
+------------------------------------------------------------------------------+
| BOND VALENCE TORSION OUT-OF- ANGLE*ANGLE |
| LENGTHS ANGLES ANGLES PLANES CROSS TERMS |
| |
| Available explicitly 48 84 121 5 141 |
| Assigned automatically 0 1 0 1 0 |
| Set to zero 0 0 0 0 3 |
+------------------------------------------------------------------------------+
*******************************************************************************
Warning: 2 Interaction Parameters were Assigned Automatically.
A detailed listing of the parameter assignments resides in the
.prm file.
*******************************************************************************
*******************************************************************************
Warning: 3 Interaction Parameters were set to Zero.
A detailed listing of the parameter assignments resides in the
.prm file.
*******************************************************************************
total time for system input and connectivity generation 0.17909 secs
Input file assignments:
-----------------------
File type
coordinate -- assigned externally.
molecular data -- assigned externally.
force field -- assigned externally.
restart -- assigned externally.
template -- assigned externally.
The random number seed is 582517.
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*Line 7 reduce *
*Line 8 ! *
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*Line 9 set dielectric = 1.000000 *
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A scalar dielectric constant of 1.0000 is being used
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*Line 10 ! *
*Line 11 ! *
*Line 12 ! *
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*Line 13 Minimize *
*Line 14 * no cross terms *
*Line 15 * no morse *
*Line 16 * for 1000 iterations *
*Line 17 * using VA09A *
*Line 18 * until the maximum derivative is less than 0.010000000 kcal/A *
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MINIMIZATION
============
Minimizer selected: BFGS.
Number of steps: 1000
Maximum derivative: 0.100E-01
A harmonic potential will be used for bond energies.
Cross term energies will not be included.
Status Before Minimization
==========================
Initial Energies
----------------
total energy components for: input file for discover
58.359673 kcal=total energy
5.663655 kcal=bond energy
16.431034 kcal=theta energy
2.980612 kcal=phi energy
0.038787 kcal=out of plane energy
0.000000 kcal=bond*bond energy
0.000000 kcal=bond*theta energy
0.000000 kcal=theta*theta energy
0.000000 kcal=bond*phi energy
0.000000 kcal=theta*phi energy
0.000000 kcal=theta*theta*phi energy
0.000000 kcal=bond*bond (1-3) energy
0.000000 kcal=op*op energy
0.000000 kcal=phi*phi energy
0.000000 kcal=hydrogen-bond energy
19.466681 kcal=nonbond energy
69.996300 kcal=non-bond repulsion energy
-50.529619 kcal=non-bond dispersion energy
13.778903 kcal=coulomb energy
0.000000 kcal=forcing potential; this contribution
has been subtracted from the total energy
Initial Derivative Summary
--------------------------
Atom Residue Molecule Derivative (kcal/mole-Angstrom)
Name Name No. Number dv/dx dv/dy dv/dz
---- -------- -------- ------------ ------------ ------------
Min: HZ2 LYSn 1 1 -0.788199 0.487884 0.076154
Max: N LYSn 1 1 13.459840 8.235775 5.194337
Average absolute derivative 2.8062123
Stand. dev. of abs. deriv. 3.0848984
RMS derivative 4.1703028
Starting minimization using BFGS
Normal completion of BFGS
---------------------
The maximum derivative criteria used was: 0.01000
The maximum derivative achieved is: 0.00843
366 iterations took 494 energy evaluations and 5.398 secs.
Time per energy evaluation is 0.011
Status After Minimization
=========================
Final Energies
--------------
total energy components for: input file for discover
30.159564 kcal=total energy
4.084407 kcal=bond energy
8.400838 kcal=theta energy
0.988260 kcal=phi energy
0.081446 kcal=out of plane energy
0.000000 kcal=bond*bond energy
0.000000 kcal=bond*theta energy
0.000000 kcal=theta*theta energy
0.000000 kcal=bond*phi energy
0.000000 kcal=theta*phi energy
0.000000 kcal=theta*theta*phi energy
0.000000 kcal=bond*bond (1-3) energy
0.000000 kcal=op*op energy
0.000000 kcal=phi*phi energy
0.000000 kcal=hydrogen-bond energy
9.922582 kcal=nonbond energy
63.382999 kcal=non-bond repulsion energy
-53.460417 kcal=non-bond dispersion energy
6.682031 kcal=coulomb energy
0.000000 kcal=forcing potential; this contribution
has been subtracted from the total energy
Final Derivative Summary
------------------------
Atom Residue Molecule Derivative (kcal/mole-Angstrom)
Name Name No. Number dv/dx dv/dy dv/dz
---- -------- -------- ------------ ------------ ------------
Min: CB LYSn 1 1 -0.000020 -0.000113 -0.000026
Max: OE1 GLUN 3 1 0.008428 0.003725 -0.006423
Average absolute derivative 0.0014757
Stand. dev. of abs. deriv. 0.0016565
RMS derivative 0.0022185
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*Line 19 ! *
*Line 20 ! *
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Total time used by DISCOVER: 5.63 second(s).
DISCOVER completed: Date: 03-Jan-99 Time: 17:26:15
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Last updated: 01/23/2001