VMD-L Mailing List

From: Gustavo Gust (gust77gust_at_gmail.com)
Date: Wed Nov 11 2009 - 10:17:37 CST

Hi John, the xst file is small, it just has the data of a,b and c in
function of time. It has 50000 frames.
My problem is when I get the data from the dcd file, I have to read the
corresponding frame from the xst file.
I don't want to split the xst file in 50000 files...

Thank you for your help,

Gustavo

On Wed, Nov 11, 2009 at 5:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Gustavo,
> Hmm, I'm not sure about that. I haven't ever read the xst reading
> code in the pbctools plugin. It's possible that's where your problem
> is originating if they are trying to read the entire xst file at once.
> How big is the xst file?
>
> Cheers,
> John
>
> On Wed, Nov 11, 2009 at 04:58:01PM +0100, Gustavo Gust wrote:
> > Hi John, I'm trying to use bigdcd (I used before) but, how can I read
> the
> > xst file, in order to get a,b and c at every frame and wrap the
> system? I
> > can't figure out how to read every frame from dcd file and the
> > corresponding data from xst file.
> > Thank you for your help.
> > Here is the script I'm trying to use with bigdcd (and probably is
> wrong,
> > but it's based in one it's working fine, without the xst file):
> > source bigdcd.tcl
> > package require pbctools
> >
> > proc nwc {frame} {
> >
> > global outfile
> >
> > pbc wrap -all <=== I need to wrap the system at every time before
> count
> > the atoms
> > pbc box
> >
> > set sel [atomselect top "(resname TIP3 and name OH2) and pbwithin 3 of
> > (resname GOL)"]
> >
> > set nw [$sel num]
> >
> > puts $fid "$frame $nw"
> >
> > }
> >
> > set fid [open "nw-file.dat" w]
> >
> > #-----------
> >
> > set dir1 "/home/gol"
> >
> > mol load psf $dir1/structure/file.psf
> >
> > pbc readxst $dir1/file.xst -all <=== it must be here or inside proc
> nwc?
> >
> > bigdcd nwc $dir1/gol.dcd
> > -----------------
> > On Wed, Nov 11, 2009 at 4:20 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >
> > Hi,
> > You're likely running VMD out of memory by loading the whole 1.9GB
> DCD
> > on
> > your system. What happens if you only load half of it? Another
> option
> > would be for you to make use of the "bigdcd" script and process it
> one
> > frame at a time.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Wed, Nov 11, 2009 at 04:04:34PM +0100, Gustavo Gust wrote:
> > > Dear colleagues,
> > > with vmd, I'm trying to use a script like this (vmd -dispdev
> text
> > -e
> > > script.tcl), which select the O atoms from TIP3 water molecules
> at
> > 3
> > > angstroms from the molecule GOL:
> > > package require pbctools
> > > set dir1 "/home/molecule/eq1"
> > > mol load psf $dir1/structure/file.psf dcd $dir1/file.dcd
> > > set nf [molinfo top get numframes]
> > > pbc readxst $dir1/file.xst -all
> > > pbc wrap -all
> > > pbc box
> > > set outfile [open file.dat w]
> > > for { set i 1 } { $i < $nf } { incr i } {
> > > set sel [atomselect top "(resname TIP3 and name OH2) and
> pbwithin 3
> > of
> > > (resname GOL)" frame $i]
> > > set nw [$sel num]
> > > puts $outfile "$i $nw"
> > > $sel delete
> > > }
> > > close $outfile
> > > Sometimes it's working fine, but frequently I get the following
> > error
> > > message:
> > > terminate called after throwing an instance of 'std::bad_alloc'
> > > what(): std::bad_alloc
> > > Abort
> > > I'm using VMD 1.8.7 and, according to former messages in the
> mail
> > list
> > > (Arneh Babakhani, Josh Stone, Feb 02 2007), I've included the
> line
> > > $sel delete
> > > but I couldn't fix this error. Also, I've tried to select
> index,
> > but it's
> > > not working anyway.
> > >
> > > Is there other alternatives or suggestions to avoid this
> problem?
> > > I'm running VMD 1.8.7 in a Linux machine with Open Suse 10.3
> and 2
> > Gb of
> > > RAM. Every dcd file has 1.9 Gb. The dimensions of the box are
> in
> > xst
> > > file.
> > > Thank you for your attention,
> > > Gustavo Velardez
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>