VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 31 2020 - 11:45:27 CDT

Hi,
  If you want to use NAMD 3 w/ NAMDPlot, you could replace this part of the
NAMDPlot code which has a modification to tolerate the typo in NAMD 3.0 alpha
output, as well as the corrected version. You would just edit the contents
of your installed NAMDPlot plugin, e.g.,
  /usr/local/lib/vmd/plugins/noarch/tcl/namdplot1.2/namdplot.tcl

You would replace the existing "namdparse" routine, with this one:

# parse NAMD output
# set foo [namdparse /home/johns/imd-glpf.log]
# examples retrieve ts value for 2nd energy output line
# puts [lindex [lindex [lindex [lindex $foo 0] 1] 1] 0]
proc ::NAMDPlot::namdparse { namdlogfilename } {
  set energydata {}
  set timingdata {}
  set energycolumns {}

  set timingcolumns [list TS "CPU Seconds" "CPU Seconds/step" \
    "Wall Seconds" "Wall Seconds/step" "Hours remaining" "kB memory in use" ]

  set infile [open $namdlogfilename "r"]
  while { [gets $infile line] >= 0 } {
    if { [regexp -- "ETITLE:" $line] } {
      set energycolumns [lrange [concat $line] 1 end]
      break
    }
  }
  set numenergycolumns [llength $energycolumns]
  while { [gets $infile line] >= 0 } {
    if { [regexp -- "ENERGY:" $line] } {
      set energies [lrange [concat $line] 1 end]
      if { [llength $energies] != $numenergycolumns } { break }
      lappend energydata $energies
    } elseif { [regexp -- "TIMING:" $line] } {
      set scnt [scan $line "TIMING:%d CPU: %f, %f/step Wall:%f,%f/step, %f hours remaining, %f %s of memory in use." ts cpusec cpusecstep wallsec wallsecstep hoursremaining meminuse memunit]
      if { $scnt < 8 } {
# set scnt [scan $line "TIMING:%d CPU: %f, %f/step Wall:%f, %f/step, %f ns/day, %f hours remaining, %f %s of memory in use." ts cpusec cpusecstep wallsec wallsecstep nsecsday hoursremaining meminuse memunit]
        set scnt [scan $line "TIMING:%d CPU: %f, %f/step Wall:%f, %f/step, %f %*s %f hours remaining, %f %s of memory in use." ts cpusec cpusecstep wallsec wallsecstep nsecsday hoursremaining meminuse memunit]
      }
      set memscale 1.0
      switch -exact $memunit {
        kB { set memscale 1.0 }
        KB { set memscale 1.0 }
        MB { set memscale 1024.0 }
        GB { set memscale [expr 1024.0 * 1024.0] }
      }
      set meminuse [expr $memscale * $meminuse]
      lappend timingdata [list $ts $cpusec $cpusecstep \
        $wallsec $wallsecstep $hoursremaining $meminuse]
    }
  }

  close $infile

  return [list \
    [list $energycolumns $energydata] \
    [list $timingcolumns $timingdata] ]
}

Best regards,
  John Stone

On Mon, Aug 31, 2020 at 04:22:36PM +0000, Kodituwakku,Dimuthu Nirmani wrote:
> Hi John,
> Yes, as my previous reply I have mistakenly mentioned NAMD 2.1.3. I used
> NAMD 3.0 to run my simulation.
> Thanks,
> Best,
> Dimuthu
>
> --------------------------------------------------------------------------
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Monday, August 31, 2020 12:02 PM
> To: Kodituwakku,Dimuthu Nirmani <dkodituwakku_at_ufl.edu>
> Cc: namd_at_ks.uiuc.edu <namd_at_ks.uiuc.edu>
> Subject: Re: Error in NAMD plot
>
> [External Email]
>
> Hi,
> The log file you posted was from NAMD 3, not from NAMD 2.x.
> NAMD 3 has a new structure that requires an updated version of the
> NAMDPlot plugin. The NAMD 3 alpha versions currently in the field also
> have a typo in the output, but hopefully this will be addressed in the
> next test builds of NAMD 3 and VMD.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Aug 30, 2020 at 04:50:50PM +0000, Kodituwakku,Dimuthu Nirmani
> wrote:
> > Hi,
> > I'm using NAMD version 2.1.3 and VMD version 1.9.3. I'm trying to use
> > namdplot on VMD but it keeps giving me the error ,
> > can't read "memunit": no such variable
> > can't read "memunit": no such variable
> > while executing
> > "switch -exact $memunit {
> > kB { set memscale 1.0 }
> > KB { set memscale 1.0 }
> > MB { set memscale 1024.0 }
> > GB { set memscale ..."
> > (procedure "namdparse" line 24)
> > invoked from within
> > "namdparse $namdlogfilename"
> > (procedure "::NAMDPlot::namdplot" line 9)
> > invoked from within
> > "::NAMDPlot::namdplot $logfile"
> > (procedure "::NAMDPlot::guiplot" line 64)
> > invoked from within
> > "::NAMDPlot::guiplot"
> > invoked from within
> > ".namdplot.menubar.file.menu invoke active"
> > ("uplevel" body line 1)
> > invoked from within
> > "uplevel #0 [list $w invoke active]"
> > (procedure "tk::MenuInvoke" line 50)
> > invoked from within
> > "tk::MenuInvoke .namdplot.menubar.file.menu 1"
> > (command bound to event)
> > Here's an example of my log file:
> > [1][IMG][2]prod9.log
> > I posted the same question in NAMD mailing list, after that I tried
> from
> > several computers with VMD for several log files and it keeps giving
> me
> > the error. So I believe there's a bug somewhere.
> > Any help would be appreciated!
> > Thanks,
> > Best,
> > Dimuthu
> >
> > References
> >
> > Visible links
> > 1.
> [1]https://urldefense.proofpoint.com/v2/url?u=https-3A__uflorida-2Dmy.sharepoint.com_-3Au-3A_g_personal_dkodituwakku-5Fufl-5Fedu_EeCNnrOlwd1PuFWeH-5FiSkPsBzELEJOYjDXZq5UT8uJhwpA-3Fe-3DJqlXEr&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=2cRvHqP6Tyswf65PzLppzw&m=OphpDGvQ2-_xf-QFW9VZYd_Em3EG8srbOtK-x7sPuPc&s=MskvODCJTjbB_lHKBBjmwcuOmJuggzxGBnyqxYqdtBk&e=
> > 2.
> [2]https://urldefense.proofpoint.com/v2/url?u=https-3A__uflorida-2Dmy.sharepoint.com_-3Au-3A_g_personal_dkodituwakku-5Fufl-5Fedu_EeCNnrOlwd1PuFWeH-5FiSkPsBzELEJOYjDXZq5UT8uJhwpA-3Fe-3DJqlXEr&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=2cRvHqP6Tyswf65PzLppzw&m=OphpDGvQ2-_xf-QFW9VZYd_Em3EG8srbOtK-x7sPuPc&s=MskvODCJTjbB_lHKBBjmwcuOmJuggzxGBnyqxYqdtBk&e=
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_-7Ejohns_&d=DwIBAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lZBrD7Kdg6WMfT4k4G6053b3wk5Pp-v-icBaFyztpxE&m=_dODVnxWyMdhUG3_A8YDTqxmQg8kmk858rOXXCTP--I&s=mqr0iOQhe36-IISTQaZkGnPT7e8Gsi1NVnEWwOlotyg&e=
> Phone: 217-244-3349
> [4]https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_&d=DwIBAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lZBrD7Kdg6WMfT4k4G6053b3wk5Pp-v-icBaFyztpxE&m=_dODVnxWyMdhUG3_A8YDTqxmQg8kmk858rOXXCTP--I&s=xslB630q2WfTKReRdPelEJrDr65jjdT_wPM0aY7ETLM&e=
>
> References
>
> Visible links
> 1. https://urldefense.proofpoint.com/v2/url?u=https-3A__uflorida-2Dmy.sharepoint.com_-3Au-3A_g_personal_dkodituwakku-5Fufl-5Fedu_EeCNnrOlwd1PuFWeH-5FiSkPsBzELEJOYjDXZq5UT8uJhwpA-3Fe-3DJqlXEr&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=2cRvHqP6Tyswf65PzLppzw&m=OphpDGvQ2-_xf-QFW9VZYd_Em3EG8srbOtK-x7sPuPc&s=MskvODCJTjbB_lHKBBjmwcuOmJuggzxGBnyqxYqdtBk&e=
> 2. https://urldefense.proofpoint.com/v2/url?u=https-3A__uflorida-2Dmy.sharepoint.com_-3Au-3A_g_personal_dkodituwakku-5Fufl-5Fedu_EeCNnrOlwd1PuFWeH-5FiSkPsBzELEJOYjDXZq5UT8uJhwpA-3Fe-3DJqlXEr&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=2cRvHqP6Tyswf65PzLppzw&m=OphpDGvQ2-_xf-QFW9VZYd_Em3EG8srbOtK-x7sPuPc&s=MskvODCJTjbB_lHKBBjmwcuOmJuggzxGBnyqxYqdtBk&e=
> 3. https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_-7Ejohns_&d=DwIBAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lZBrD7Kdg6WMfT4k4G6053b3wk5Pp-v-icBaFyztpxE&m=_dODVnxWyMdhUG3_A8YDTqxmQg8kmk858rOXXCTP--I&s=mqr0iOQhe36-IISTQaZkGnPT7e8Gsi1NVnEWwOlotyg&e=
> 4. https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_&d=DwIBAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lZBrD7Kdg6WMfT4k4G6053b3wk5Pp-v-icBaFyztpxE&m=_dODVnxWyMdhUG3_A8YDTqxmQg8kmk858rOXXCTP--I&s=xslB630q2WfTKReRdPelEJrDr65jjdT_wPM0aY7ETLM&e= 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/