VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 24 2011 - 12:14:39 CDT

On Tue, 2011-05-24 at 18:19 +0200, maria goranovic wrote:
> Thank you Ajasja. This worked. However, now I have a segmentation
> fault after 604 frames. Cannot figure out this one at all ... ??

are you creating selections with atomselect and not deleting them?

axel.

> On Tue, May 24, 2011 at 4:48 PM, Ajasja Ljubetič
> <ajasja.ljubetic_at_gmail.com> wrote:
> Hi,
>
>
> since bigdcd loads one frame from memory processes it and then
> deletes it you only have one frame loaded.
> Try changing the line
> set sel [atomselect $molid "name OW and within $cut of
> ($seltext)" frame $i]
> to
> set sel [atomselect $molid "name OW and within $cut of
> ($seltext)"]
>
> and also delete
> $sel frame $i
>
>
> In general you have to be change any selection where you
> are referencing the frame number.
>
>
> Best regards,
> Ajasja
>
>
> On Tue, May 24, 2011 at 15:39, maria goranovic
> <mariagoranovic_at_gmail.com> wrote:
> Hi
>
>
> I am trying to use Justin's script closewater.tcl to
> find the closest 1000 water molecules to the protein
> in each frame of the trajectory. Although this works
> perfectly, my trajectory is too big for vmd to handle
> (16,000 frames of 85,000 atoms, no velocities). So, I
> thought of combining bigdcd.tcl to closewater.tcl to
> get the data out. This needed some minor modifications
> in closewater.tcl. I have the following problem
> though.
>
>
> closewater.tcl reads in the entire trajectory, and
> calculates the number of waters using the following:
>
>
> set sel [atomselect $molid "name OH2 and within $cut
> of ($seltext)" frame $i]
>
>
> (where molid is 0)
>
>
> when I use bigdcd, I call closewater using only the
> frame number, and get the following error:
>
>
> bigdcd aborting at frame 3
> atomsel: frame 3 out of range for molecule 0
>
>
> How can this be sorted out?
>
>
> I am attaching the entire script that is being use
> below:
>
>
> ##############################################
> mol load gro temp.gro
> source mybigdcd.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 3000
> set prefix "close"
> set wat [atomselect $molid "name OW"]
> if { [$wat num] < $nwat } {
> error "Molecule contains ony [wat $num] water
> molecules."
> }
> # set nframes [molinfo $molid get numframes]
> # puts "the number of frames is $nframes"
> # for { set i 0 } { $i < $nframes } { incr i } {
> 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)" frame $i]
> set outer [$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"
> # take all waters from inner, and just enough from
> outer
> 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)"]
> $sel frame $i
> set j [format %06d $i]
> # $sel writepdb [format $prefix-%04d.pdb $i]
> $sel writepdb [format $prefix-$j.pdb]
> $sel delete
> # }
> }
>
>
> bigdcd closewater temp.xtc
> bigdcd_wait_till_done
>
>
> ##############################################
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
>
>
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.