From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Tue Sep 25 2007 - 22:24:48 CDT
Hello,
As I re-read my questions at the end of the email, I find that the
second question could be clearer. I am going to try and rephrase and
see if this makes it more clear. Questions are marked with **
As always, I appreciate and look forward to hearing from the NAMD community.
Let us consider the last line that I pasted in my previous email:
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
** Does each number in in this entry correspond to a value in ETITLE?
I am pretty sure that the 120 corresponds to the timestep, but was
unable to find in the userīs guide or the tutorial any information as
to what the entries meant for the "run" part of a simulation (as
opposed to a minimization).
Let us consider now the pressure entry:
PRESSURE: 120 269.419 -209.936 531.515 -209.936 -288.44 59.5893
531.515 59.5893 -157.572
** Again, I am pretty sure that the first number corresponds to the
time step, but what do the other numbers correspond to? Is the
program giving multiple pressures?
In the end, I hope to be able to plot total energy, pressure and
temperature as a function of time. I think that I should be able to
do this by extracting the relevant information from the log file. Is
there something wrong with my approach?
Thank you in advance.
Audrey
On 9/25/07, Audrey Salazar <alsalazar_at_northwestern.edu> wrote:
> 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
>
>
-- 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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