VMD에서 사용하는 TCL script

자세한건 http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node7.html

Data Analysis of DCD result file

Open the script file distance.tcl with a text editor. You can see that the script does the following:

• Choose atom selections 
  set sel1 [atomselect top "$seltext1"] 
  set sel2 [atomselect top "$seltext2"] 
  

• Get the number of frames in the trajectory and assign this value to the variable nf 
  set nf [molinfo top get numframes] 
  

• Open file specified by the variable f_r_out 
  set outfile [open $f_r_out w] 
  

• Loop over all frames 
  for {set i 0} {$i < $nf} {incr i} { 
  

• Write out the frame number and update the selections to the current frame 
  puts "frame $i of $nf" 
  $sel1 frame $i 
  $sel2 frame $i 
  

• Find the center of mass for each selection (com1 and com2 are position vectors) 
  set com1 [measure center $sel1 weight mass] 
  set com2 [measure center $sel2 weight mass] 
  

• At each frame i, find the distance by subtracting one vector from the other (command vecsub) and computing the length of the resulting vector (command veclength), assign that value to an array element simdata($i.r), and print a frame-distance entry to a file 
  set simdata($i.r) [veclength [vecsub $com1 $com2]] 
  puts $outfile "$i $simdata($i.r)" 
  } 
  

• Close the file 
  close $outfile 
  

• The second part of the script is for obtaining the distance distribution. It starts from finding the maximum and minimum values of the distance 
  set r_min $simdata(0.r) 
  set r_max $simdata(0.r) 
  for {set i 0} {$i < $nf} {incr i} { 
  set r_tmp $simdata($i.r) 
  if {$r_tmp < $r_min} {set r_min $r_tmp} 
  if {$r_tmp > $r_max} {set r_max $r_tmp} 
  } 
  

• The step over the range of distances is chosen based on the number of bins N_d defined in the beginning, and all values for the elements of the distribution array are set to zero 
  set dr [expr ($r_max - $r_min) /($N_d - 1)] 
  for {set k 0} {$k < $N_d} {incr k} { 
  set distribution($k) 0 
  } 
  

• The distribution is obtained by adding 1 (incr ...) to an array element every time the distance is within the respective bin 
  for {set i 0} {$i < $nf} {incr i} { 
  set k [expr int(($simdata($i.r) - $r_min) / $dr)] 
  incr distribution($k) 
  } 
  

• Write out the file with the distribution 
  set outfile [open $f_d_out w] 
  for {set k 0} {$k < $N_d} {incr k} { 
  puts $outfile "[expr $r_min + $k * $dr] $distribution($k)" 
  } 
  close $outfile 

Visualization data file for LAMMPS input

topo readlammpsdata system.data full 

animate write psf system.psf