From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Sep 25 2007 - 22:58:19 CDT
Hi Audrey,
The numbers in each line correspond to these:
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
TS is Time Step, BOND is bond energies, ANGLE is angle energies, and so forth. All of these quantities are as described in any book that discusses MDS, such as Leach's book on modeling.
Energy values are in kcal/mol. BOUNDARY energy is from spherical boundary conditions and harmonic restraints,
while MISC energy is from external electric fields and various steering forces.
TOTAL is the sum of the various potential energies, and the KINETIC energy.
TOTAL2 uses a slightly different kinetic energy that is better conserved
during equilibration in a constant energy ensemble.
TOTAL3 is another variation with much smaller short-time fluctuations that
is also adjusted to have the same running average as TOTAL2.
Defects in constant energy simulations are much easier to spot in TOTAL3
than in TOTAL or TOTAL2.
Pressure values are in bar. Temperature values are in Kelvin.
PRESSURE is the pressure calculated based on individual atoms, while
GPRESSURE incorporates hydrogen atoms into the heavier atoms to which
they are bonded, producing smaller fluctuations.
The TEMPAVG, PRESSAVG, and GPRESSAVG are the average of temperature and
pressure values since the previous ENERGY output; for the first step
in the simulation they will be identical to TEMP, PRESSURE, and GPRESSURE.
The sign of the pressure depends upon how one looks at it. I believe it's negative because it's the pressure acting ON the system.
Hope this helps,
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN
55414-2959
rwoodphd_at_yahoo.com
Hastings, MN
rwoodphd_at_yahoo.com
----- Original Message ----
From: Audrey Salazar <alsalazar_at_northwestern.edu>
To: namd-l_at_ks.uiuc.edu
Sent: Tuesday, September 25, 2007 9:08:31 PM
Subject: namd-l: Meaning of lines in "run" part of log file.
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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