VMD-L Mailing List

From: bo liu (liubo.njuer_at_gmail.com)
Date: Thu May 15 2008 - 13:00:23 CDT

Hi guys

Thanks for sharing!

What I did with namdplot is adding tcl lines to namdplot.tcl in VMD package:

 set f [open dat.dat w]
   foreach i $xarr j $arr {
       puts $f [format "%10d %17.4f" $i $j]
   }
 close $f
  # format the title, having the plotter allow a legend would be nice

I have modified my namdplot.tcl,and I found this is a much convinient way
for me to extract data using namdplot plugin.

Just one more idea to manipulate data with VMD!

Cheers!

2008/5/15 Subramanian Vaitheeswaran <vaithee_at_umd.edu>:

> Hi Alexander,
>
> This script is indeed very useful, thank you!
>
> Vaithee
> ============================================
> S. Vaitheeswaran
> Post-doctoral Research Associate
> Institute for Physical Science & Technology
> Rm 2116, Bldg. 85
> University of Maryland
> College Park MD 20742
> email: vaithee_at_umd.edu
> Phone: 301-405-7568
> ============================================
>
>
>
> ---- Original message ----
> >Date: Thu, 15 May 2008 08:11:19 +0500
> >From: "Alexandre A. Vakhrouchev" <makaveli.lcf_at_gmail.com>
> >Subject: namd-l: Energy plot script
> >To: namd-l_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu
> >
> >Hi all!
> >
> >Long long time ago I've made energy plotting script using NAMD
> >logfile. May be it will be usefull for community)
> >See it atached. Only tool it requires is gnuplot. It also produces
> >*.dat files containing cols of extracted data, so every one can use
> >his preffered plotting tool)
> >
> >--
> >Best regards,
> >
> >Dr. Alexander Vakhrushev
> >Institute of Applied Mechanics
> >Dep. of Mech. and Phys.-Chem.
> >of heterogeneous mediums
> >UB of Russian Academy of Sciences
> >34 T. Baramzinoy St.
> >Izhevsk, Russia 426067
> >________________
> >plot_energy.sh.gz (2k bytes)
>
> 

-- 
-Liu bo
-----------------------------------------------------------
Computational Biology, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
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