VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Mon Oct 27 2008 - 14:01:21 CDT

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
>
>