VMD-L Mailing List

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Wed May 05 2010 - 13:57:16 CDT

Hi Ajasja,

Thank you for reply!

Because I have a trajectory whose format is not readable for vmd, so I have
to generate pdb files first and then load them to vmd. I tried bigdcd like
this:

#############################
source bigdcd.tcl

proc output { frame } {
puts "#: $frame"
}

set start 0
set end 499
set stride 10
set fileformat "%06d0.00ps.pdb"

set filename [format $fileformat 0]
set mol [mol new $filename type pdb waitfor all]

for {set i $start} {$i <= $end} {incr i 1} {

    set filename [format $fileformat [expr $i]]
        bigdcd output pdb $filename
        bigdcd_wait
}

quit

################################

But the memory problem is still there!

Thanks,

Wei

On Wed, May 5, 2010 at 12:44 AM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com>wrote:

> Hello,
> have you looked at this<http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/>script already? So that you do not have to extract the trajectory to PDBs.
> Does the memory usage differ if you use
>
> animate delete beg $thisframe end $thisframe $mol
>
> To delete the frames?
>
> Regards,
>
> Ajasja
>
>
> On Wed, May 5, 2010 at 00:07, Wei Chen <cwbluesky_at_gmail.com> wrote:
>
>> Hi all,
>>
>> I try to load a series of pdb files, which were extracted from a
>> trajectory. In order to save memory, I load one at a time and delete it
>> using "animate delete all" before loading the second one. It indeed saved
>> some memory, but the memory usage still keeped increasing when I loaded
>> hundreds pdb files. Could anybody tell me what is wrong? Is it because other
>> information than coordinates from pdb files is not deleted when using
>> "animate delete all"?
>>
>> My script is as follows:
>>
>> *************************************************************
>> set start 0
>> set end 499
>> set stride 10
>> set fileformat "%06d0.00ps.pdb"
>>
>> for {set i $start} {$i <= $end} {incr i 1} {
>> set filename [format $fileformat [expr $i]]
>> if {$i == $start} {
>> set molid [mol new $filename type pdb waitfor all]
>> puts "molid = $molid"
>> } else {
>> animate read pdb $filename waitfor all $molid
>> }
>>
>> animate delete all
>> puts "delete $filename"
>>
>> }
>>
>> quit
>> ************************************************************
>>
>> Thank you!
>>
>> Wei Chen
>>
>
>