Re: vmd-l: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...)

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 16 2008 - 07:20:26 CDT

The usual advice on tcl scripting is not to unset atom selections, but
to delete them:
$selection delete

The tcl garbage collector can take care of anything that isn't an atom
selection.

BTW, if you're going to cross-post betwee namd and vmd-l, please at
least make it the same email to make it easier for one reply to
propagate to both lists (better, though, to pick the most appropriate
list rather than cross post).

Best, Peter

bo liu wrote:
> Dear All
>
> I'm trying to compute water dipole orientations inside a nanotube.
> Water dipole orientation along the channel should be averaged for
> positions and the data should be averaged over the trajectory.
> I write a tcl script (See below, Also attached) for VMD to do this,
> but when i source the script, it quickly uses up all the memory
> resources so that
> i can only deal with no more than 5 frames...
>
> i have followed tips on tcl scripting to unset the variables when i am
> finished with them, but the prolem remains...
> i have no idea what is going wrong... NEED YOUR HELP!
>
> Many Thanks!
>
> the script:
>
> # output water dipole orientation, averaged along the nanotube.
> # water's fallin-region:
> # (z>0.0)&&(z<33.0)&&((x-0.12)*(x-0.12)+(y+0.13)*(y+0.13)<36)
> #
> ####################################################################
>
> set tcl_precision 6
> ####################################################################
> # calculate cosine value from a dipole vector
> proc get_cos id {
>
> # create one selection of atoms from the resid number
> set sel [atomselect top "resid $id"]
>
> # get dipole vector
> set dipole_vec [measure dipole $sel]
> unset sel
>
> # get z component of dipole_vector
> set z [lindex $dipole_vec 2]
>
> # calculate the cosine value from the length and z component
> set scale [veclength $dipole_vec]
> set cos [expr $z / $scale]
> unset dipole_vec
> return $cos
> }
> ####################################################################
> # in oder to average the data of water dipole orientations along the
> # tube, the nanotube is divided into 50 slices, refer to 50 slots
> # in which cosine values of water dipole orentation should be filled.
> # return 50 lists, each list corresponds to a specific region along
> # the tube.
> #
> # determine which slots should be filled in, return slots' id list
> proc allocate z {
> if {($z >= 0.66) && ($z < 1.32)} {
> return {1 2 3}
> }
> if {($z >= 1.32) && ($z < 1.98)} {
> return {2 3 4}
> }
> if {($z >= 1.98) && ($z < 2.64)} {
> return {3 4 5}
> }
> if {($z >= 2.64) && ($z < 3.3)} {
> return {4 5 6}
> }
> if {($z >= 3.3) && ($z < 3.96)} {
> return {5 6 7}
> }
> if {($z >= 3.96) && ($z < 4.62)} {
> return {6 7 8}
> }
> if {($z >= 4.62) && ($z < 5.28)} {
> return {7 8 9}
> }
> if {($z >= 5.28) && ($z < 5.94)} {
> return {8 9 10}
> }
> if {($z >= 5.94) && ($z < 6.6)} {
> return {9 10 11}
> }
> if {($z >= 6.6) && ($z < 7.26)} {
> return {10 11 12}
> }
> if {($z >= 7.26) && ($z < 7.92)} {
> return {11 12 13}
> }
> if {($z >= 7.92) && ($z < 8.58)} {
> return {12 13 14}
> }
> if {($z >= 8.58) && ($z < 9.24)} {
> return {13 14 15}
> }
> if {($z >= 9.24) && ($z < 9.9)} {
> return {14 15 16}
> }
> if {($z >= 9.9) && ($z < 10.56)} {
> return {15 16 17}
> }
> if {($z >= 10.56) && ($z < 11.22)} {
> return {16 17 18}
> }
> if {($z >= 11.22) && ($z < 11.88)} {
> return {17 18 19}
> }
> if {($z >= 11.88) && ($z < 12.54)} {
> return {18 19 20}
> }
> if {($z >= 12.54) && ($z < 13.2)} {
> return {19 20 21}
> }
> if {($z >= 13.2) && ($z < 13.86)} {
> return {20 21 22}
> }
> if {($z >= 13.86) && ($z < 14.52)} {
> return {21 22 23}
> }
> if {($z >= 14.52) && ($z < 15.18)} {
> return {22 23 24}
> }
> if {($z >= 15.18) && ($z < 15.84)} {
> return {23 24 25}
> }
> if {($z >= 15.84) && ($z < 16.5)} {
> return {24 25 26}
> }
> if {($z >= 16.5) && ($z < 17.16)} {
> return {25 26 27}
> }
> if {($z >= 17.16) && ($z < 17.82)} {
> return {26 27 28}
> }
> if {($z >= 17.82) && ($z < 18.48)} {
> return {27 28 29}
> }
> if {($z >= 18.48) && ($z < 19.14)} {
> return {28 29 30}
> }
> if {($z >= 19.14) && ($z < 19.8)} {
> return {29 30 31}
> }
> if {($z >= 19.8) && ($z < 20.46)} {
> return {30 31 32}
> }
> if {($z >= 20.46) && ($z < 21.12)} {
> return {31 32 33}
> }
> if {($z >= 21.12) && ($z < 21.78)} {
> return {32 33 34}
> }
> if {($z >= 21.78) && ($z < 22.44)} {
> return {33 34 35}
> }
> if {($z >= 22.44) && ($z < 23.1)} {
> return {34 35 36}
> }
> if {($z >= 23.1) && ($z < 23.76)} {
> return {35 36 37}
> }
> if {($z >= 23.76) && ($z < 24.42)} {
> return {36 37 38}
> }
> if {($z >= 24.42) && ($z < 25.08)} {
> return {37 38 39}
> }
> if {($z >= 25.08) && ($z < 25.74)} {
> return {38 39 40}
> }
> if {($z >= 25.74) && ($z < 26.4)} {
> return {39 40 41}
> }
> if {($z >= 26.4) && ($z < 27.06)} {
> return {40 41 42}
> }
> if {($z >= 27.06) && ($z < 27.72)} {
> return {41 42 43}
> }
> if {($z >= 27.72) && ($z < 28.38)} {
> return {42 43 44}
> }
> if {($z >= 28.38) && ($z < 29.04)} {
> return {43 44 45}
> }
> if {($z >= 29.04) && ($z < 29.7)} {
> return {44 45 46}
> }
> if {($z >= 29.7) && ($z < 30.36)} {
> return {45 46 47}
> }
> if {($z >= 30.36) && ($z < 31.02)} {
> return {46 47 48}
> }
> if {($z >= 31.02) && ($z < 31.68)} {
> return {47 48 49}
> }
> if {($z >= 31.68) && ($z < 32.34)} {
> return {48 49 50}
> } else {
> return {49 50 51}
> }
> }
> ####################################################################
> # determine the numerator for averaging
> proc sum list {
> set sum 0
> foreach i $list {
> set sum [expr {$sum+$i}]
> }
> set sum
> }
>
> ####################################################################
> set numFrame [molinfo top get numframes]
> set wat [atomselect top "name OH2"]
> # get index list of water
> set index [$wat get index]
> unset wat
> # create lists for data storage.
> for {set i 1} {$i <= 50} {incr i} {
> set list$i {}
> }
> ####################################################################
> for {set fr 0} {$fr < $numFrame} {incr fr} {
> echo "\$\$\$\$\$ [expr $numFrame - $fr] frames left! \$\$\$\$\$"
>
> molinfo top set frame $fr
> foreach wt_num $index {
> # get atomselection
> set wt_atom [atomselect top "index $wt_num"]
> # get {x y z}
> set sx [lindex [$wt_atom get x] 0]
> set sy [lindex [$wt_atom get y] 0]
> set sz [lindex [$wt_atom get z] 0]
>
> # search fallin water molecules
> if {($sz > 0.0) && ($sz < 33.0) && (($sx - 0.12)*($sx - 0.12)
> + ($sy + 0.13)*($sy + 0.13) < 36)} {
>
> set resid [$wt_atom get resid]
> echo "Water:$resid falls in"
> set cos_value [get_cos $resid]
>
> # refresh lists
>
> foreach i [allocate $sz] {
> lappend list$i $cos_value
> echo $cos_value
> }
> unset resid cos_value
> }
> unset wt_atom sx sy sz
> }
> }
> #######################################
> # lists manipulation, output
> set f [open water_profile.data a+]
> for {set i 1} {$i <= 50} {incr i} {
> set numerator [sum [set list$i]]
> set denominator [llength [set list$i]]
> if {$denominator != 0} {
> set average [expr $numerator / $denominator]
> } else {
> set average 0
> }
> puts $f [format %8f $average]
> }
> close $f
> puts "done!"
>
>
> --
> -Liu bo
> -----------------------------------------------------------
> Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
> College of Chemistry and Chemical Engineering, Graduate University of
> Chinese Academy of Sciences, Beijing P.R. China
> Office: (86)-010-88233187
> Home: (86)-010-88259765
> Cell: 13426057875
>
>
>
> --
> -Liu bo
> -----------------------------------------------------------
> Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
> College of Chemistry and Chemical Engineering, Graduate University of
> Chinese Academy of Sciences, Beijing P.R. China
> Office: (86)-010-88233187
> Home: (86)-010-88259765
> Cell: 13426057875

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