From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Tue Sep 25 2007 - 20:08:31 CDT
Dear NAMD-L,
I am new to NAMD and have recently starting to play with the program.
I ran an NPT simulation with 100 minimization steps and 1000 run
(equilibration) steps. In my config file, I request the following
output:
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 20
xstFreq 20
outputEnergies 20
outputPressure 20
I am now including a part of my log file. My snippet includes the
last time step of the minimization run and the first 2 time steps of
the equilibration.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 100 474.5487 343.5259 84.6759
0.3343 -15574.5321 1060.9264 0.0000
0.0000 0.0000 -13610.5209 0.0000
-13610.5209 -13610.5209 0.0000 -7759.3056
-6334.5498 45520.3692 -7759.3056 -6334.5498
WRITING COORDINATES TO DCD FILE AT STEP 100
REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
TCL: Running for 1000 steps
PRESSURE: 100 -2652.49 96.4711 -6.98656 96.4711 -3123.69 163.778
-6.98656 163.778 -3147.84
GPRESSURE: 100 -2716.6 230.975 111.683 -199.216 -3072.16 156.778
58.806 242.102 -3045.39
ENERGY: 100 27.5801 54.4359 84.6615
0.3337 -14188.3019 1043.2132 0.0000
0.0000 2577.7860 -10400.2916 312.0522
-10397.8918 -10406.8912 312.0522 -2974.6758
-2944.7148 45520.3692 -2974.6758 -2944.7148
PRESSURE: 120 269.419 -209.936 531.515 -209.936 -288.44 59.5893
531.515 59.5893 -157.572
GPRESSURE: 120 203.993 -196.666 477.228 -114.099 -219.93 -52.7689
551.267 132.735 -4.20402
PRESSAVG: 120 95.154 211.163 259.725 211.163 -250.506 76.5522 259.725
76.5522 -190.837
GPRESSAVG: 120 187.637 203.971 261.961 247.167 -293.61 94.6072 285.943
77.4568 -246.008
ENERGY: 120 31.3348 78.8359 93.6109
1.5920 -14223.7686 1416.3426 0.0000
0.0000 2264.0462 -10338.0063 274.0726
-10334.4953 -10340.9442 264.6460 -58.8642
-6.7135 44994.3063 -115.3965 -117.3267
After reading this,
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node10.html
it is pretty clear that each number for the minimization step output
corresponds to each of the numbers in ETITLE. I.e. TS=100,
DIHED=84.6759, PRESSAVG=-6334.5498.
** How and why are these pressures negative?
** What do the multiple numbers mean for each line mean? I.e. if we
look at the last ENERGY line, the 120 probably refers to the time
step. What do the rest of the numbers mean? I could ask the same
question for the PRESSURE line, as well.
Thank you in advance.
Audrey
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node25.html#ap-stdout
It is pretty clear that the
-- Audrey L. Salazar Amaral Research Group Dept. of Chemical and Biological Engineering Phone: 847.491.2188 Northwestern University Evanston, IL USA
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