VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jun 07 2011 - 09:02:10 CDT

Hi,

it depends on how you call it. If you use vmd -eofexit -e " " then it should
exit. You can also just put an exit statement at the end.

Regards,
Ajasja

On Tue, Jun 7, 2011 at 11:01, maria goranovic <mariagoranovic_at_gmail.com>wrote:

> Dear All,
>
> I have a vmd script (copied below) which I would expect to exit after
> finishing, but it does not. Any ideas why? version 1.9, linux, amd64
>
>
>
> mol load gro all.gro
> source mybigdcd2.tcl
>
> # closewater.tcl
> # Justin Gullingsrud
> # jgulling_at_mccammon.ucsd.edu
> # 8 November 2004
>
> # This script processes a trajectory to create a new file containing just
> # a selection of atoms and the N closest water to that selection. The N
> # waters are recomputed for each timestep, and need not be the same waters
> # in each timestep (in fact, they probably will not be); thus it is in
> general
> # meaningless to analyze the dynamics of individual waters. However, it
> # may be useful for analyzing the distribution of waters around a
> relatively
> # static protein or DNA chain.
>
> # usage: closewater <molid> <selection text> <# waters> <filename prefix>
>
> proc closewater {i} {
>
> set molid 0
> set seltext "protein"
> set nwat 2500
> set prefix "close"
> puts "now working in frame $i"
> set numinner 0
> set inner [list]
> set cut 1
> while {1} {
> set sel [atomselect $molid "name OW and within $cut of ($seltext)"]
> set outer [$sel list]
> $sel delete
> set numouter [llength $outer]
> if { $numouter < $nwat } {
> set inner $outer
> set numinner $numouter
> incr cut
> continue
> }
> break
> }
> puts "Found $numouter waters at cutoff $cut"
> catch { unset ohash }
> foreach ind $outer { set ohash($ind) 1 }
> foreach ind $inner { unset ohash($ind) }
> set outer [lrange [array names ohash] 0 [expr $nwat - $numinner - 1]]
> set watind [concat $inner $outer]
> set sel [atomselect $molid "($seltext) or same residue as (index
> $watind)"]
> set j [format %06d $i]
> $sel writepdb [format $prefix-$j.pdb]
> exec editconf -f $prefix-$j.pdb -o $prefix-$j.gro -resnr 1 &
> }
> bigdcd closewater temp.xtc
> bigdcd_wait_till_done
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>