VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Wed Oct 29 2008 - 15:16:08 CDT

Hi John,

I have tried to use less atoms to do the alignment but there was still no
convergence problems.
No peptide has ever crossed the boundary of the box.
I also tried to first center every frame of the peptide and then do the
calculation, but I also get the no convergence error.
Below I attached the tcl script. Can you have a look to see is there
anything I am doing wrong?

Jianhui

a8an_pep_min3-6_ctr.dcd is the trajectory for Ac-AAAAAAAA-Nme centered.

############################################################################################
# This code is used to calculated mean square displacement of peptide.

#####################################
# Second do the MSD calculation.
set dcdFile2 a8an_pep_min3-6_ctr.dcd

mol new
/.automount/polaris/home/tianj/tianj/selfassemble_rmakUA_080429/aklocation/built/a8_md1_last
_ctr.pdb type pdb 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
animate delete beg 0 end 0

set num_frames [molinfo top get numframes]

set sel1 [atomselect top "backbone"]
set sel2 [atomselect top "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 0} {$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
#########################################################################################

On Mon, Oct 27, 2008 at 5:35 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Try using a smaller subset of atoms to do your alignment and
> see if you can get a successful alignment. By excluding any that
> may have wrapped over a periodic boundary, you may get a decent
> transformation matrix, and then you'd be able to apply it to
> all of the atoms.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Oct 27, 2008 at 03:01:21PM -0400, Jianhui Tian wrote:
> > Hi,
> >
> > Can anyone give any suggestions? Thanks.
> >
> > Jianhui
> >
> > On Fri, Oct 24, 2008 at 6:02 PM, Jianhui Tian <jianhuitian_at_gmail.com>
> wrote:
> >
> > > 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
> > >
> > >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>