VMD-L Mailing List

From: Robert Brunner (rbrunner_at_illinois.edu)
Date: Wed Jun 03 2009 - 13:48:49 CDT

You still have your "$water delete" and "$lipids delete" outside of
the block where they are created. You should probably have them
immediately after "set Nlipids [llength [lsort -integer -unique
[$lipids get residue]]]" since that is the last point where the
selection is used.

You are making a new atom selection every time you go through the
loop, but you are only freeing the last one you make when you leave
the loop.

Robert

On Jun 3, 2009, at 12:54 PM, Alberto Sergio Garay wrote:

> Dear Axel Kohlmeyer
>
> I have checked my script following your recommendation:
>
>> you may have mixed up loop nesting!
>> memory leaks in this kind of scripting almost
>> always (= 99%) are due to forgotten or
>> overwritten(!) selections.
>
> But I could not find any mistake so I'm pasting a part of the script
> which when it is run takes some of the ram memory and never leaves
> it until
> I close vmd.
>
> BTW, I'm waiting for my password in order to be able to up my md
> gromacs trayectory files(gro and xtc ) for testing the script.
>
> Thank you in advance
>
> #Script to look for some molecules around (radius) a particular
> residue (resid) in all the
> #periodic replicas of the principal box of simulation and move them
> close to it.
> #The script is thought to work on lipids bilayers.
>
> proc rsel {resid radius} {
> set num_steps [molinfo top get numframes]
>
> for {set n 0} {$n <= $num_steps} {incr n 1} {
>
> puts "calculation on frame $n"
>
> #Taking the box dimension
> set Xbox [lindex [pbc get] 0 0]
> set Ybox [lindex [pbc get] 0 1]
> set Zbox [lindex [pbc get] 0 2]
>
> #Setting the coordinates of the target residue
> set sx [[atomselect top "resid $resid" frame $n] get {x} ]
> set sy [[atomselect top "resid $resid" frame $n] get {y} ]
> set sz [[atomselect top "resid $resid" frame $n] get {z} ]
>
> #Calculating the min-max dimention of the selected molecule
> set minx [lindex $sx 0]
> set miny [lindex $sy 0]
> set minz [lindex $sz 0]
> set maxx $minx
> set maxy $miny
> set maxz $minz
> foreach x $sx y $sy z $sz {
> if {$x < $minx} {set minx $x} else {if {$x > $maxx} {set maxx $x}}
> if {$y < $miny} {set miny $y} else {if {$y > $maxy} {set maxy $y}}
> if {$z < $minz} {set minz $z} else {if {$z > $maxz} {set maxz $z}}
> }
>
> #Calculation of geometric centre
> set centre_X [expr ($minx + $maxx) / 2]
> set centre_Y [expr ($miny + $maxy) / 2]
> set centre_Z [expr ($minz + $maxz) / 2]
> set cg "$centre_X $centre_Y $centre_Z"
>
> #Moving the geometric centre to each periodic box and###
> #Making a list of water molecules inside the defined sphere
> for {set i 1} {$i <= 3} {incr i} {
> if {$i == 1} {set X $centre_X}
> if {$i == 2} {set X [expr $centre_X - $Xbox]}
> if {$i == 3} {set X [expr $centre_X + $Xbox]}
> for {set j 1} {$j <= 3} {incr j} {
> if {$j == 1} {set Y $centre_Y}
> if {$j == 2} {set Y [expr $centre_Y - $Ybox]}
> if {$j == 3} {set Y [expr $centre_Y + $Ybox]}
> for {set k 1} {$k <= 3} {incr k} {
> if {$k == 1} {set Z $centre_Z}
> if {$k == 2} {set Z [expr $centre_Z - $Zbox]}
> if {$k == 3} {set Z [expr $centre_Z + $Zbox]}
>
>
> set water [atomselect top "same residue as (resname SOL) and ((x-
> ($X))*(x-($X)) + (y-($Y))*(y-($Y)) + (z-($Z))*(z-($Z))) < ($radius*
> $radius)" frame $n]
> set lipids [atomselect top "same residue as (resname DMP) and ((x-
> ($X))*(x-($X)) + (y-($Y))*(y-($Y)) + (z-($Z))*(z-($Z))) < ($radius*
> $radius)" frame $n]
>
> #Moving the selected molecules close to the target
>
> if {$i == 2} {$water moveby "$Xbox 0 0"
> $lipids moveby "$Xbox 0 0"}
> if {$i == 3} {$water moveby "-$Xbox 0 0"
> $lipids moveby "-$Xbox 0 0"}
> if {$j == 2} {$water moveby "0 $Ybox 0"
> $lipids moveby "0 $Ybox 0"}
> if {$j == 3} {$water moveby "0 -$Ybox 0"
> $lipids moveby "0 -$Ybox 0"}
> if {$k == 2} {$water moveby "0 0 $Zbox"
> $lipids moveby "0 0 $Zbox"}
> if {$k == 3} {$water moveby "0 0 -$Zbox"
> $lipids moveby "0 0 -$Zbox"}
>
> set Nwater [llength [lsort -integer -unique [$water get residue]]]
> set Nlipids [llength [lsort -integer -unique [$lipids get residue]]]
> if {$Nwater > 0} { puts "water molec found: $Nwater" }
> if {$Nlipids > 0} { puts "lipids molec found: $Nlipids" }
>
> }
> }
> }
>
> $water delete
> $lipids delete
>
> #Making a new selection around the selected residue
> set water [atomselect top "same residue as (resname SOL) and ((x-
> ($centre_X))*(x-($centre_X)) + (y-($centre_Y))*(y-($centre_Y)) + (z-
> ($centre_Z))*(z-($centre_Z))) < ($radius*$radius)" frame $n]
> set lipids [atomselect top "same residue as (resname DMP) and ((x-
> ($centre_X))*(x-($centre_X)) + (y-($centre_Y))*(y-($centre_Y)) + (z-
> ($centre_Z))*(z-($centre_Z))) < ($radius*$radius)" frame $n]
>
> #Here should be start the Hbonds calculation
>
> $water delete
> $lipids delete
>
>
> }
> puts "End of calculation..."
> }
>
>
>
> --
> Dr. Sergio Garay
> Facultad de Bioquimica y Cs. Biológicas
> Universidad Nacional del Litoral
> Santa Fe - Argentina
> C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
> Argentina
> Ph. +54 (342) 4575-213
> Fax. +54 (342) 4575-221
>
>
>
>
>