VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Tue Aug 29 2006 - 04:46:24 CDT

hey wang,

I do not know exactly, but might it be that vmd ran out of memory and crashed?
To me it looks like your script might have a memory leak,
because you do not delete and unset the selections after usage within the loop.
So try either

$all delete; unset all

within the loop, or (that is better) use update.

Are you sure that all frames were loaded (no "waitfor all")?

try that:
###############
mol new all.psf type psf waitfor all
mol addfile 1.dcd type dcd waitfor all

set nf [molinfo top get numframes]
set all [atomselect top all frame 0]

 for {set i 0 } {$i < $nf} {incr i}
 {
     $all frame $i
     $all update
     $all writepdb $i.pdb
 }
$all delete; unset all

################

eddi

On Tuesday 29 August 2006 08:27, wang wrote:
> Dear all ,
> I used VMD software to transform dcd file (from NAMD) into pdb format file .
> There are 30000 frames in dcd file . But I only tranfromed 4500 pdb files .
> Could you tell me how to fix the problem ?
> thx
> wang ^^
>
>
> my script
> _____________________________________________________
> mol load psf all.psf dcd 1.dcd
> set nf [molinfo top get numframes]
> for {set i 0 } {$i < $nf} {incr i}
> {
> set all [atomselect top all frame $i ]
> $all writepdb $i.pdb
> }
>
> 

-- 
--
=============================================================================
Eduard Schreiner                     e-mail: eduard.schreiner_at_theochem.rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                              http://www.theochem.rub.de
=============================================================================