VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Tue Aug 29 2006 - 02:41:47 CDT

also since you redefine the variable "all" with each iteration you may
run out of memory before your script completes, a better script would
be...

mol load psf all.psf dcd 1.dcd
set nf [molinfo top get numframes]
set all [atomselect top all]
for {set i 0 } {$i < $nf} {incr i} {
    $all frame $i
    $all writepdb $i.pdb
}

On 8/29/06, dimka <newyorkdimka_at_gmail.com> wrote:
> ran out of quota/disk space? file is greater than 2gb and operating
> system cannot support >2gb files...
>
> On 8/29/06, wang <c00jsw00_at_nchc.org.tw> 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
> > }
> >
> >
>