VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jun 08 2011 - 03:33:23 CDT

Ajasja, Using -eofexit or using an exit statement at the end of file do not
work in this case.

On Tue, Jun 7, 2011 at 4:07 PM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com>wrote:

> 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
>>>
>>
>>
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen