VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Feb 01 2016 - 21:12:45 CST

Thanks Peter!

What you are telling is true but then I will be generating enormous amount
of pdb files which I also don't want to do. Isn't there any other method ?

Best,
Monika

Monika Madhavi
Department of Physics
University of Colombo
On Feb 2, 2016 12:51 PM, "Peter Freddolino" <petefred_at_umich.edu> wrote:

> Dear Monika,
> The atom selections are not constructed on a frame by frame basis. You can
> update them with $sel update, but at the time that the animate write
> command is issued, only their current state will be considered. You can
> solve this easily enough just by looping over frames and writing a separate
> pdb file for each of them.
> Best,
> Peter
>
> > On Feb 1, 2016, at 7:01 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
> >
> > Dear all,
> >
> > I want to create some atomselections, update them every frame and write
> the coordinates to a pdb file. I need to create a pdb file for each atom
> selection (which includes updated coordinates for all frames). Below is the
> code I wrote. The code works but, the selections are not updated. In the
> pdb files, there are coordinates of the same atom selection. Can you please
> suggest a way to correct this.
> >
> > Thank you.
> > Best regards,
> > Monika
> >
> > proc intermol1 {n} {
> > #reading tracer atoms from a file
> > set input [open "myout.dat" r]
> > set atomlist [read $input]
> > set len [llength $atomlist]
> > #
> > #select tracer atoms one by one
> > for {set i 0} {$i < $len} {incr i} {
> > set fname [format "interout%03d" $i]
> > set ind1 [lindex $atomlist $i]
> > set ind2 [expr $ind1+1]
> > #
> > #load trajectory frame by frame
> > set mol [mol new my.psf type psf waitfor all]
> > for {set frm 0} {$frm < $n} {incr frm} {
> > mol addfile ../my.dcd type dcd first $frm last $frm waitfor all molid
> $mol
> > #
> > set centH1 [atomselect $mol "index $ind1" frame $frm]
> > set coorH1 [lindex [$centH1 get {x y z }] 0]
> > set x0 [lindex $coorH1 0]
> > set y0 [lindex $coorH1 1]
> > set z0 [lindex $coorH1 2]
> > $centH1 delete
> > #select H in a 5A sphere
> > set sel1 [atomselect $mol "name H1 H2 and
> sqrt(sqr(x-x0)+sqr(y-y0)+sqr(z-z0))<5 and not index $ind2" frame $frm]
> > $sel1 update
> > }
> > animate write pdb $fname.pdb beg 0 end [expr $n-1] waitfor all sel $sel1
> $mol
> > animate delete beg 0 $mol
> > $sel1 delete
> > }
> > }
> >
> > --
> > W.A.Monika Madhavi
> > Lecturer (Probation),
> > Department of Physics,
> > University of Colombo.
>
>