VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jun 07 2011 - 09:07:08 CDT

Sorry, it should be:
 vmd -dispdev text -eofexit < input.tcl > output.log

Regards,
Ajasja

On Tue, Jun 7, 2011 at 16:02, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>wrote:

> 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
>>
>
>