Advanced VMD Script Examples and Customization

Transcription

1 Advanced VMD Script Examples and Customization Axel Kohlmeyer Center for Molecular Modeling University of Pennsylvania SBS JNCASR, Bangalore

2 The Real Power of VMD VMD is a tool for visualization of (bio-)molecular data and allows to generate high-quality images VMD is a tool for analysis of (bio-)molecular data VMD is a tool for preparing inputs and controlling (bio)-molecular simulations VMD is through script interface(s) customizable Powerful new functionality can be added without recompilation and (mostly) scripts Its design encourages creativity, collaboration and cooperation.

3 The VMD Data Model Molecule 0 Structure Data / Topology Volumetric Data Sets Trajectory Data, Coordinates + User data (per frame) Molecule 1 Structure data / Topology...and so on Trajectory Data, Coordinates

4 The VMD Visualization Model Molecule 0 Representation 1 Labels Representation 0: Atom Selection (default: all) Drawing Method (Lines) Coloring Method (Name) Material (Opaque) Periodicity, Frame Selection Molecule 1 Representation 0...and so on Custom Graphics Objects

5 Changing Defaults with.vmdrc Upon startup VMD looks for a file.vmdrc which can contain TCL script code Some possible customizations: menu main on ; # should be always on menu graphics on ; # shows rep dialog after idle { menu tkcon on } axes location off display resize mol default style VDW ; # VDW not Lines mol default selection protein

6 Changing Defaults with.vmdrc More.vmdrc customizations: display projection orthographic color Display Background silver user add key o \ {display projection orthographic} user add key p \ {display projection perspective} user add key d { \ if {[display get rendermode]!= "Normal" }\ {display rendermode Normal}\ {display rendermode GLSL} }

7 How to Tell VMD to Load Your Custom Commands on Demand 1) Put your TCL extensions in a common directory, e.g., ${HOME}/vmd/myscripts 2) Extend the TCL variable $auto_path: set auto_path [concat \ $env(home)/vmd/myscripts $auto_path] 3) Create a tclindex file (in VMD console): cd ~/vmd/myscripts auto_mkindex. *.tcl 4) Now VMD will automatically load the matching TCL script if you use a command that is defined in a script in this directory.

8 Custom VMD Command Example proc hardcopy { {renderer "TachyonInternal"}} { # set the background temporarily to white to save ink set oldbg [colorinfo category Display Background] color Display Background white set tga {/tmp/.hardcopy.tga} set ps {/tmp/.hardcopy.ps} render $renderer $tga exec convert $tga $ps exec lpr $ps exec rm -f $tga $ps color Display Background $oldbg }

9 How to Show Bond-Breaking and Bond-Formation By default VMD assumes that bonds stay the same throughout a trajectory -> heritage in classical MD Combining a VDW representation (at scale 0.2) with a Dynamic Bonds representation allows to recompute bonds on the fly. With multiple average bond lengths and atom types, use multiple representations with selections

10 Adding Graphics Objects Put a sphere at the origin: draw color yellow draw sphere {0 0 0} radius.5 graphics returns an id that can be used to selectively delete objects: set c [draw cylinder {0 0 0}\ {5 0 0} radius.5] draw delete $c Coordinates refer to the coordinate system of the molecule loaded

11 Adding Dynamical Graphics TCL allows to monitor objects (e.g. variables) with the trace command VMD provides several traceable variables that one can tap into proc do_time {args} { display_time_bar "fs" 0 } set mol [molinfo top] trace variable vmd_frame($mol) \ w do_time

12 Using External Data for Graphics 1) Extract total dipole moment from first principles CPMD simulation: awk '{ print $2, $3, $4; }' \ DIPOLE > zundel.dip 2) Read dipole vector into array and 3) compute & store center of mass: set dip [open "zundel.dip" r] set sel [atomselect 0 "not name X"] set nf [molinfo 0 get numframes] for {set i 0} {$i < $nf} {incr i} { $sel frame $i set dipdata($i) [list [measure center $sel] [gets $dip]] } close $dip

13 Using External Data for Graphics 4) Hook up function to draw dipole vector graphics to $vmd_frame. proc do_dipdraw {args} { global dipdata dipgraph set mol [molinfo top] ; set frame [molinfo $mol get frame] if {[info exists dipdata($frame)]} then { if {[info exists dipgraph]} then { foreach g $dipgraph { graphics $mol delete $g } } graphics $mol color yellow lassign $dipdata($frame) cnt vec set dipgraph [vmd_draw_vector $mol \ $cnt $vec ] }} trace variable vmd_frame(0) w do_dipdraw

14 Using a Computed User Value Colorization shall indicate deformation of C60 molecules set mol [molinfo top] set left [atomselect $mol {index < 60}] set right [atomselect $mol {index>= 60}] set nf [ molinfo $mol get numframes ] for {set i 0} {$i < $nf} {incr i} { $left frame $i set com [measure center $left] set dlist "" foreach c [$left get {x y z}] { lappend dlist [veclength [vecsub $c $com]] } $left set user $dlist # repeat for second molecule... }

15 Using VMD to Tailor Data In LAMMPS trajectories are PBC are applied per-atom in output We can use VMD to make molecules whole again: set mol [molinfo top] set ring [atomselect $mol {type 3}] set nf [molinfo $mol get numframes] for {set i 0} {$i < $nf} {incr i} { make_whole $mol $ring $i 8 }

16 Using VMD to Tailor Data proc make_whole {mol sel frame num} { molinfo $mol set frame $frame $sel frame $frame set allcoord [$sel get {x y z}] set num1 [expr {$num - 1}] set boxhalf [vecscale 0.5 [molinfo $mol get {a b c}]] set newcoord {} while {[llength $allcoord] > 0} { set coord [lrange $allcoord 0 $num1] set allcoord [lrange $allcoord $num end] set ref [lindex $coord 0] lappend newcoord $ref foreach atom [lrange $coord 1 end] { set newatom {} set dist [vecsub $atom $ref] foreach d $dist b $boxhalf r $atom { if {$d < -$b} { set r [expr {$r + 2.0*$b}]} if {$d > $b} { set r [expr {$r - 2.0*$b}]} lappend newatom $r } lappend newcoord $newatom } } $sel set {x y z} $newcoord )

17 For More Information Join VMD (Public) project on BioCoRE Use the Source, Luke! (Translation: read and learn from the many available VMD/TCL scripts).