VMD-L Mailing List

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Thu Feb 26 2009 - 15:57:56 CST

Hi John,

Thank you for your help. But I changed the code but the problem is still there:

set dcdfile C:/test.dcd
set outfile [open rmsd.dat w]
mol addfile $dcdfile type dcd first 0 last 0 step 1 filebonds off
autobonds off waitfor all
set frame0 [atomselect top "name N" frame 0]
# rmsd calculation loop
for { set i 100 } { $i <= 200 } { incr i } {
        mol addfile $dcdfile type dcd first $i last $i step 1 filebonds off
autobonds off waitfor all
        set sel [atomselect top "name N"]
        $sel frame $i
        $sel move [measure fit $sel $frame0]
        puts $outfile "$i [measure rmsd $sel $frame0]"
        puts $i
        $sel delete
}
close $outfile

Thank you!

Fred

On Thu, Feb 26, 2009 at 4:16 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
>  It looks like you're failing to delete the atom selections
> you're creating in your script.  You need to have a
> call to "$sel delete" inside that loop...  That's probably
> one of the reasons your memory use is not going down much.
> Also, you should put the "frame0" selection and molecule
> loading outside of the loop, otherwise you're killing your
> machine...
>
> Cheers,
>  John
>
> On Thu, Feb 26, 2009 at 04:00:53PM -0500, Fred (Rui FENG) wrote:
>> Hi All,
>>
>> The manual says when tcl command "animate delete all" is executed, VMD
>> will delete all the frames from the memory. But when I check the
>> memory from the Windows Task Manager, the memory doesn't reduce much.
>> Because I'm trying to read a 2.4 GB dcd file frame by frame to
>> calculate RMSD, VMD will use up the memory. The Tcl code is below:
>>
>> # codes start
>> set dcdfile C:/test.dcd
>> set outfile [open rmsd.dat w]
>>
>> # rmsd calculation loop
>> for { set i 100 } { $i <= 200 } { incr i } {
>>       animate delete all
>>       mol addfile $dcdfile type dcd first 0 last 0 step 1 filebonds off
>> autobonds off waitfor all
>>       set frame0 [atomselect top "name N" frame 0]
>>
>>       mol addfile $dcdfile type dcd first $i last $i step 1 filebonds off
>> autobonds off waitfor all
>>       set sel [atomselect top "name N"]
>>       $sel frame $i
>>       $sel move [measure fit $sel $frame0]
>>       puts $outfile "$i [measure rmsd $sel $frame0]"
>>       puts $i
>> }
>> close $outfile
>> animate delete all
>> # codes end
>>
>> Do you know how to slove the out-of-memory problem? Thank you!
>>
>> Have a nice day!
>>
>> Fred
>
> --
> 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
>