Standard Dynamics Cascade
Information
 
Status
Success
 
User
16606
Elapsed Time
00:02:49
Start
09/15/22 10:51:04
Finish
09/15/22 10:53:53
Server Name
AbdusemiAbduweli
DS Version
19.1.0.18287
PP Version
19.1.0.1963
DS Client Version
19.1.0.18287
Server Ports
9944 (9943)
OS Distribution
Windows
OS Version
10.0.22000
Memory Total
23.85 GB
Memory Free
14.14 GB
Warnings
No periodic boundary condition defined. Turning constant pressure off.
Production Type changed from NPT to NVT.
Summary
Spherical Cutoff method is used for electrostatics.
Name Stage Forcefield Start Time (ps) End Time (ps) Initial Potential Energy (kcal/mol) Total Energy (kcal/mol) Potential Energy (kcal/mol) Kinetic Energy (kcal/mol) Temperature (K) Van der Waals Energy (kcal/mol) Electrostatic Energy (kcal/mol) Initial RMS Gradient (kcal/(mol x A)) Final RMS Gradient (kcal/(mol x A))
1YRF Minimization CHARMm     -2355.369   -2500.566     -256.290 -1643.843 11.715 0.908
1YRF Minimization2 CHARMm     -2500.566   -2574.063     -263.858 -1500.762 0.908 0.165
1YRF Heating CHARMm 0.000 4.000 -2574.063 -1757.554 -2185.048 427.494 290.317 -222.762 -1319.776 1.472 18.964
1YRF Equilibration CHARMm 4.000 14.000 -2185.048 -1728.785 -2184.258 455.473 309.318 -185.431 -1284.526 18.964 18.635
1YRF Production CHARMm 14.000 24.000 -2184.258 -1738.416 -2190.207 451.791 306.817 -192.239 -1049.459 18.635 19.393
Results
CHARMm Log File
Energy Table
Output Molecule
Output Molecule Without Conformations
Parameters
Protocol Settings
Protocol.pr_xml
 
Input Typed Molecule
1YRF.dsv
Minimization
Algorithm
Steepest Descent
Max Steps
1000
RMS Gradient
1.0
Constraints
Minimization2
Algorithm
Conjugate Gradient
Max Steps
2000
RMS Gradient
0.1
Constraints
Heating
Simulation Time (ps)
4
Time Step (fs)
2
Initial Temperature
50.0
Target Temperature
300.0
Adjust Velocity Frequency
50
Save Results Interval (ps)
2
Constraints
Equilibration
Simulation Time (ps)
10
Time Step (fs)
2
Target Temperature
300.0
Adjust Velocity Frequency
50
Save Results Interval (ps)
2
Constraints
Production
Simulation Time (ps)
10
Time Step (fs)
2
Target Temperature
300.0
Temperature Coupling Decay Time
5.0
Save Results Interval (ps)
2
Save Restart File
True
Constraints
Type
NVT
TMass
1000.0
PMass
1000.0
PGamma
25.0
Reference Pressure
1.0
Implicit Solvent Model
Generalized Born
Dielectric Constant
1
Implicit Solvent Dielectric Constant
80
Generalized Born Lambda Constant
Minimum Hydrogen Radius
0.8
Use Non-polar Surface Area
True
Non-polar Surface Constant
0.92
Non-polar Surface Coefficient
0.00542
Salt Concentration
0.0
Input Atomic Radii
van der Waals radii
Use Molecular Surface
True
Nonbond List Radius
14.0
Nonbond Higher Cutoff Distance
12.0
Nonbond Lower Cutoff Distance
10.0
Electrostatics
Automatic
Kappa
0.34
Order
4
Advanced
Dynamics Integrator
Leapfrog Verlet
Apply SHAKE Constraint
True
Random Number Seed
314159 314159 314159 314159
Number of Processors
1
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