VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Fri Oct 24 2008 - 17:02:08 CDT

Hi,

I found out there was one post regarding this problem before. From my
understanding, that problem was because of the peptide cross the boundary of
the unit cell.
In my calculation, I don't encounter such situation.

What I did was:
I wrote a script to calculate the RMSD between every two frames of a
trajectory for a peptide.
The peptide was located in the center of the box for the most of time and
its configuration was fluctuating (not really folding/unfolding).
And I got warning as following:
Matrix: Warning: no convergence (0.00001000<505.03359985 after 1000
iterations).
 Matrix: Warning: no convergence (0.00001000<434.05392456 after 1000
iterations).
 Matrix: Warning: no convergence (0.00001000<484.80929565 after 1000
iterations).

I am also including my little script here. Thanks in advance.
# This code is used to calculated "mean square displacement" of protein.

set dcdFile2 ../a8an_rm14_min3.dcd

mol new
/.automount/polaris/home/tianj/tianj/selfassemble_rmakUA_080429/aklocation/a8an_rm14.prmtop

type parm7 first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol addfile $dcdFile2 type dcd first 0 last -1 step 1 filebonds 1 autobonds
1 waitfor all

set num_frames [molinfo top get numframes]

set sel1 [atomselect top "protein and backbone"]
set sel2 [atomselect top "protein and backbone"]

set file2 [open "temp" "w"]
set file1 [open "rmsd_t" "w"]
# R(t)^2=1/(trun-t)*sum_(trun-t){[x(td+t)-x(td)]^2}
# Loop through t.
for {set deltai 1} {$deltai < $num_frames} {incr deltai} {
  # Loop through td.
  set totmsd 0
  set totrmsd 0
  set sumframes [expr $num_frames -$deltai]
  for {set i 1} {$i < $sumframes} {incr i} {
    set j [expr $i + $deltai]
    $sel1 frame $i
    $sel2 frame $j

    #compute the transformation
    set trans_mat [measure fit $sel2 $sel1]
    #do the alignment
    $sel2 move $trans_mat
    set trmsd [measure rmsd $sel1 $sel2]
    set totmsd [expr $totmsd + $trmsd * $trmsd]
    set totrmsd [expr $totrmsd + $trmsd]
    puts $file1 [list $i $trmsd]
  }
  set msd [expr $totmsd/$sumframes]
  set rmsd [expr $totrmsd/$sumframes]
  puts $file2 [list $deltai $msd $rmsd]
}

exit