From: Molecular Dynamics (moleculardynamics_at_yahoo.com)
Date: Wed Mar 21 2012 - 04:19:57 CDT
Dear namd experts,
I want to
perform 10 ns md simulation for 1000 record in NVT ensamble for analysis of the
system. To do this I searched for restart files and examined lots of files
which are different from each other. Then I generated a restart conf file that
starts from the last step in namd.out file . But I’m confused about restart
procedure. And I’m not sure if my restart conf file is true for 10 ns with 1000
record . So I need an expert help . Could you please look over the attached conf
file and share your thoughts with me ?
Best
regards.
WRITING EXTENDED SYSTEM TO RESTART FILE
AT STEP 2512500
WRITING COORDINATES TO DCD FILE AT STEP
2512500
WRITING COORDINATES TO RESTART FILE AT
STEP 2512500
FINISHED WRITING RESTART COORDINATES
The last position output (seq=2512500)
takes 0.006 seconds, 869.734 MB of memory in use
WRITING VELOCITIES TO RESTART FILE AT
STEP 2512500
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=2512500)
takes 0.004 seconds, 869.734 MB of memory in use
WRITING FORCES TO DCD FILE AT STEP
2512500
The last force output (seq=2512500) takes
0.001 seconds, 868.934 MB of memory in use
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT
STEP 2512500
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT
STEP 2512500
CLOSING COORDINATE DCD FILE
The last position output (seq=-2) takes
0.087 seconds, 869.355 MB of memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP
2512500
CLOSING FORCE DCD FILE
The last velocity output (seq=-2) takes
0.070 seconds, 868.676 MB of memory in use
====================================================
WallClock: 151413.078125 CPUTime: 151413.078125 Memory: 868.675781 MB
End of program
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