VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue May 24 2011 - 11:19:26 CDT

Thank you Ajasja. This worked. However, now I have a segmentation fault
after 604 frames. Cannot figure out this one at all ... ??

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