Re: Energy Plugin

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 05 2006 - 13:46:24 CST

Hi Bo,
it looks like the first error is occuring because either csh or namddat
isn't in the proper place. If you could, please try running
csh namddat
and let me know the results (no need to copy to namd-l). If it fails
please also send me the results of the command
which csh

The reason that namdplot-2 isn't working is simply that the newly
created file doesn't have execute permissions set. If you run
chmod u+x namdplot-2

and then try running namdplot-2 again, it should work.
Please let me know if things still don't work after trying this.
Best,
Peter

bo baker wrote:

>Hello, Peter:
>
>I can't make the 'namddat' to work on the Mac computer. It has some
>format problem. The command can't be recongized. Here is how I did:
>
>[mriv209-01:~] bo% cd desktop
>[mriv209-01:~/desktop] bo% setenv PATH .:$PATH
>[mriv209-01:~/desktop] bo% ./namddat N62-2.log
>tcsh: ./namddat: Command not found.
>
>I then try the 'namdplot' downloaded previously with 'scripts.dmg',
>and extracted into my local directory. It works fine:
>
>[mriv209-01:~/desktop] bo% ./namdplot TEMP N62-2.log
>ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC
>TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
>GPRESSAVG
>Plotting TEMP vs TS
>[1] 1842
>
>
>When I try to modify the 'namdplot', to add two lines from your
>'namddat' using 'vi' from 'terminal' window:
>-----
>echo $xtitle $ytitle >! data.dat
>cat $tmpfile >> data.dat
>-----
>
>and then save the it as 'namdplot-2'. Then load it :
>
>[mriv209-01:~/desktop] bo% ./namdplot-2 N62-2.log
>tcsh: ./namdplot-2: Permission denied.
>[mriv209-01:~/desktop] bo%
>
>
>It seems that the 'namdplot-2' is modified by the computer, and no
>longer be recognized. I have included the two files as attachemntd. I
>use Mac OSX 10.3.9, and I have the X-11 loaded.
>
>Thanks for any suggestions
>
>bo
>
>
>On 1/3/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
>
>>Dear Bo,
>>in this case you'll probably want to use namddat (attached here for your
>>convenience). This is exactly like namdplot, but it extracts the
>>energies to a file called data.dat instead of trying to print it. You
>>can then load data.dat into excel to plot it. Please let me know if you
>>have any problems with this.
>>Best,
>>Peter
>>
>>bo baker wrote:
>>
>>
>>
>>>Dear Peter:
>>>
>>>Thank you for the information.
>>>
>>>
>>>
>>>
>>>
>>>>However, I am curious what you mean by saying the energy information is
>>>>in a ---.log file. If all you want to do is extract energy information
>>>>
>>>>
>>>>from a preexisting log file, you are better off just using existing
>>>
>>>
>>>>shell tools (I can give you more details if you need).
>>>>
>>>>
>>>>
>>>>
>>>I just want to extract energy information from the .log file. I try
>>>to use 'namdplot', but I don't have 'gramcx' in the computer. I use
>>>Mac OSX. Can you give me more details for the shell tool? So I can
>>>extract the energy to a text file, then plot it using other program,
>>>such as Excel?
>>>
>>>Thank you for advice.
>>>
>>>Bo
>>>
>>>On 1/2/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>>>
>>>
>>>
>>>
>>>>Dear Bo,
>>>>NAMDEnergy is not fully implemented in VMD 1.8.3. If you want to use it
>>>>
>>>>
>>>>from the console, you should run the commands
>>>
>>>
>>>>package require namdenergy
>>>>namdenergy
>>>>
>>>>to get usage instructions. A more mature version of NAMDEnergy is
>>>>included in VMD 1.8.4; there is also a GUI available in this version.
>>>>You can download this version from the VMD website.
>>>>
>>>>However, I am curious what you mean by saying the energy information is
>>>>in a ---.log file. If all you want to do is extract energy information
>>>>
>>>>
>>>>from a preexisting log file, you are better off just using existing
>>>
>>>
>>>>shell tools (I can give you more details if you need). NAMDEnergy is
>>>>designed to do new simulations to calculate the energies of subsystems,
>>>>which cannot be obtained from the logfile of a prior run.
>>>>
>>>>Peter
>>>>
>>>>bo baker wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Hello, NAMD:
>>>>>I am condused on how to make the "NAMD Energy Plugin" to work in VMD?
>>>>>The energy information is in a ---.log file. I go to 'console', what
>>>>>is the command should I type? I use VMD 1.8.3. There is no "NAMD
>>>>>Energy Plugin" under "Extension - Analysis'.
>>>>>
>>>>>Thank you for your help
>>>>>
>>>>>Bo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>#!/bin/csh
>>
>># Written in 1999 by Jim Phillips, Theoretical Biophysics Group,
>># Beckman Institute, University of Illinois at Urbana-Champaign.
>>
>>if ( $#argv < 1 ) then
>> echo "Usage: $0 [zero] [diff] [<yfield> [<yfield> ...] [vs <xfield>]] <file>"
>> exit -1
>>endif
>>
>>set titles = `awk '/^ETITLE:/ { print; exit }' $argv[$#argv]`
>>echo $titles
>>
>>if ( $#argv < 2 ) then
>> echo "Usage: $0 [zero] [diff] [<yfield> [<yfield> ...] [vs <xfield>]] <file>"
>> exit -1
>>endif
>>
>>if ( $1 == zero ) then
>> set zero = 1
>> shift argv
>>else
>> set zero = 0
>>endif
>>
>>if ( $1 == diff ) then
>> set zero = 1
>> set diff = 1
>> shift argv
>>else
>> set diff = 0
>>endif
>>
>>set ytargets =
>>while ( $#argv > 1 && $1 != vs )
>> @ pos = 1
>> foreach t ( $titles )
>> if ( $t == $1 ) set ytargets = ( $ytargets $pos )
>> @ pos++
>> end
>> shift argv
>>end
>>
>>if ( $#ytargets == 0 ) exit -1
>>
>>set xtarget = 2
>>if ( $1 == vs ) then
>> shift argv
>> @ pos = 1
>> foreach t ( $titles )
>> if ( $t == $1 ) set xtarget = $pos
>> @ pos++
>> end
>> shift argv
>>endif
>>
>>set file = $argv[1]
>>
>>set ytitle =
>>foreach y ( $ytargets )
>> set ytitle = ( $ytitle $titles[$y] )
>>end
>>set xtitle = $titles[$xtarget]
>>
>>#echo Plotting $ytitle vs $xtitle
>>echo Calculating average of $ytitle
>>
>>set title = $file
>>
>>set open = '{'
>>set close = '}'
>>set dollar = '$'
>>
>>if ( $zero ) then
>> set subtitle = "change from initial value"
>> set prog = "NR == 1 $open"
>> foreach y ( $ytargets )
>> set prog = "$prog z$y = $dollar$y;"
>> end
>> set prog = "$prog $close"
>> set prog = "$prog $open print $dollar$xtarget"
>> foreach y ( $ytargets )
>> set prog = "$prog, $dollar$y - z$y"
>> end
>> set prog = "$prog $close"
>> if ( $diff ) then
>> set subtitle = "running backward difference"
>> set prog = "$prog $open"
>> foreach y ( $ytargets )
>> set prog = "$prog z$y = $dollar$y;"
>> end
>> set prog = "$prog $close"
>> endif
>>else
>> set subtitle = ""
>> set prog = "$open print $dollar$xtarget"
>> foreach y ( $ytargets )
>> set prog = "$prog, $dollar$y"
>> end
>> set prog = "$prog $close"
>>endif
>>
>>
>>#echo $prog
>>
>>set quote = '"'
>>set p_title = "TITLE $quote$title$quote"
>>set p_subtitle = "SUBTITLE $quote$subtitle$quote"
>>set p_xaxis = "XAXIS LABEL $quote$xtitle$quote"
>>
>>set tmpfile = /tmp/namdplot.$USER.$$.tmp
>>
>>set l_cmd = ( 0 0 0 0 0 0 0 0 0 0 )
>>@ pos = 1
>>foreach t ( $ytitle )
>> @ i = $pos - 1
>> set l_cmd[$pos] = "S$i LEGEND $quote$t$quote"
>> @ pos++
>>end
>>
>>while ( $pos <= 10 )
>> set l_cmd[$pos] = "S$i LEGEND $quote$t$quote"
>> @ pos++
>>end
>>
>>grep '^ENERGY:' $argv | grep -v '[a-z]' | awk "$prog" > $tmpfile
>>
>>
>>
>>set ys=`echo $ytitle | awk '{print NF}'`
>>#echo $ys
>>
>>echo $xtitle $ytitle >! data.dat
>>cat $tmpfile >> data.dat
>>
>>#set j=2
>>#while ( $j < $ys + 2 )
>># echo $j
>># set av=`tail +102 $tmpfile | awk -v i=$j 'BEGIN{sum=0}{sum+= $i} END{print sum/NR}' `
>># set k=`expr $j - 1`
>># echo " $ytitle[$k] \t $av"
>># @ j++
>>#end
>>
>>
>>
>>
>>#xmgrace \
>># -pexec "LEGEND on" \
>># -pexec "$l_cmd[1]" \
>># -pexec "$l_cmd[2]" \
>># -pexec "$l_cmd[3]" \
>># -pexec "$l_cmd[4]" \
>># -pexec "$l_cmd[5]" \
>># -pexec "$l_cmd[6]" \
>># -pexec "$l_cmd[7]" \
>># -pexec "$l_cmd[8]" \
>># -pexec "$l_cmd[9]" \
>># -pexec "$l_cmd[10]" \
>># -pexec "$p_title" -pexec "$p_subtitle" -pexec "$p_xaxis" \
>># -pexec "XAXIS TICKLABEL FORMAT DECIMAL" -pexec "XAXIS TICKLABEL PREC 0" \
>># -pexec "YAXIS TICKLABEL FORMAT DECIMAL" -pexec "YAXIS TICKLABEL PREC 0" \
>># -autoscale xy -remove -nxy $tmpfile &
>>
>>
>>
>>
>>

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