From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Sep 26 2007 - 10:16:42 CDT
Audrey,
For the "PRESSURE:" line, the nine numbers following the time step
(120) give the 3x3 pressure tensor listed by row. Similarly for the
"GPRESSURE:" line.
-Dave
On Sep 26, 2007, at 9:55 AM, Audrey Salazar wrote:
> Hello,
> Thank you all for answering most of my questions. I am still
> wondering what the PRESSURE line means (an example follows):
>
> PRESSURE: 120 269.419 -209.936 531.515 -209.936 -288.44 59.5893
> 531.515 59.5893 -157.572
>
> There are not as many entries as ETITLE. Which one of these pressures
> is the one that I care about? What do these numbers represent?
>
> Thank you in advance
>
> Audrey
>
> On 9/26/07, Richard Swenson <swenson_at_hec.utah.edu> wrote:
>> Audrey,
>>
>> If you want to extract the energy data from your log file and
>> store it into
>> a new file, you can use the awk program from the command line and
>> redirect
>> the output to a file.
>>
>> awk -v timestep=.002 '/ENERGY: / {print $2*timestep" "$12}'
>> logfile > ouptut
>>
>>
>> You can change the $12 to correspond to any term in the energy
>> line (ie. $3
>> for bond energy, $4 for angle energy, $5 for dihedral energy, and
>> so on).
>>
>> This is just an alternative to other equally valid ways already
>> posted,
>>
>> Richard
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
>> On Behalf
>> Of Audrey Salazar
>> Sent: Tuesday, September 25, 2007 9:25 PM
>> To: namd-l_at_ks.uiuc.edu
>> Subject: Re: namd-l: Meaning of lines in "run" part of log file.
>>
>> 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/node1
>> 0.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/node2
>> 5.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
>>
>>
>>
>>
>
>
> --
> Audrey L. Salazar
> Amaral Research Group
> Dept. of Chemical and Biological Engineering Phone: 847.491.2188
> Northwestern University
> Evanston, IL USA
----------------------------------------------------------
David J. Hardy, PhD
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/
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