VMD-L Mailing List

From: Kos (asimplefunguy_at_netscape.net)
Date: Wed May 04 2005 - 11:14:22 CDT

Hi,
I wrote a script(eg probigdcd.tcl) as a solution to use/source
it before bigdcd.tcl:

#############
proc myrmsd { frame } {
set outfile [open rms0.dat a+];
  global ref sel all
  $all move [measure fit $sel $ref]
  puts $outfile "$frame: [measure rmsd $sel $ref]"
close $outfile
}

mol load psf protein_water.psf

set ref [atomselect top "protein and backbone and noh" frame 0]
set sel [atomselect top "protein and backbone and noh"]
animate read dcd bpti1.dcd beg 0 end 0
set all [atomselect top all]
#############

It compares every frame (rmsd) with the first frame of the trajectory and
write the results in the file rms0.dat.
If someone likes could compare a custom frame with the rest of the trajectory also.

Regards,Kos

asimplefunguy wrote:

>Hi,
>I'd like to use the 'bigdcd' script
>http://www.ks.uiuc.edu/Research/vmd/script_library/
>but in order:
>
>-to compare with the first(or custom) frame of the trajectory 'frame0'
>-and to write everything in the file 'RMSD plot vs numframes'
>-to select backbone:
>'set frame0 [atomselect top "protein and backbone and noh" frame 0]'
>
>Could anyone help since I'm not so familiar with the script language?
>We'll name this file 'rms_inicustom.tcl' and someone could source it
>before 'source bigdcd.tcl'
>
>Regards,Kos
>
>
>
>John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
>
>>
>>And in case you haven't read my previous email, there _IS_ a way to run
>>VMD in text mode:
>>  vmd -dispdev text
>>
>
>>
>>The text mode way of running VMD won't use much less memory than the
>>full graphics mode.  Most of the memory consumed is for storing the
>>trajectory data.  If you load the data, the memory will be used, simple
>>as that.  If you need to save memory, then use the 'bigdcd' script to
>>process your trajectories a frame at a time.
>>
>>  John

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