VMD-L Mailing List

From: alexandra.marques_at_fc.up.pt
Date: Fri Aug 25 2006 - 05:38:06 CDT

Hi

I based in the sasa.tcl script to write a script to calculate the gyration
radius over simulation time. I wonder if someone could tell me if my script is
correct...or have any suggestion to improve it.

set outfile [open rgyr.txt w]
set nf [molinfo top get numframes]
set all [atomselect top "resid 1 to 255"]
for {set i 0} {$i<$nf} {incr i} {
$all frame $i
$all update
set rgyr [measure rgyr $all]
puts $outfile "Frame $i, rgyr $rgyr"
}
close $outfile

Thanks in advance
Alex

Quoting Marc Charendoff <mcharend_at_sbcglobal.net>:

> Hey All,
>
> After wrestling with the *.gro file end-of-file issue
> I though about the situation...
>
> 1. Some files I appended arbitrary box vectors to
> revealed structures in VMD that looked "smeared."
>
> 2. Some .gro files I couldn't view regardless of the
> box vectors I inserted.
>
> 3. GROMACs exploded on initial energy minimization
> run.
>
> 4. VMD kept on giving me "unexpected end-of-file"
> errors.
>
> On a whim, I woke up this morning and resaved my text
> *.gro files under the option "MS DOS with LIne Breaks"
> and voila' I'm up and running. Just wanted to post
> this for those in the future (although I think they
> will probably be much brighter than I) and thank the
> moderators for putting up with me.
>
> Regards, Marc
>

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