Re: Meaning of lines in "run" part of log file.

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Sep 26 2007 - 00:38:00 CDT

Audrey,

You are right about the fact that each entry in ENERGY: corresponds to a
value in ETITLE.

There is a script called namdplot (see under scripts in the NAMD website)
that you can use to plot any
value, given its name as it appears in the ETITLE line. Alternatively, I
have a perl script that I have written
that does the same. If you want, I can pass it to you. (I wrote my own since
there was something buggy about the namdplot script I got from the NAMD
site..

Cheers,

Arun

On 9/26/07, Audrey Salazar <alsalazar_at_northwestern.edu> wrote:
>
> 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 userĀ“s 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
>
>

-- 
***********************************************
Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Japan
Phone: +81 (0)235-29-0824
Email: krishnan_at_ttck.keio.ac.jp
URL: http://www.iab.keio.ac.jp/~krishnan
**********************************************

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