From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Mar 21 2011 - 03:36:15 CDT

You're missing

$sel frame $frame in the proc "myrmsd". You have to tell the selection from
which frame to take the coordinates.

(A very similar problem was discussed here very recently)

Regards,
Ajasja

On Mon, Mar 21, 2011 at 04:38, jnsong <jnsong_at_itcs.ecnu.edu.cn> wrote:

> Dear all,
>
> I've tried to use bigdcd.tcl analyses a big NAMD trajectory, but I got
> the following results:
>
> ----------------------
> 1 0.0
> 2 0.0
> 3 0.0
> 4 0.0
> 5 0.0
> 6 0.0
> 7 0.0
> 8 0.0
> 9 0.0
> 10 0.0
> 11 0.0
> 12 0.0
> 13 0.0
> -----------------------
>
> rmsd for each frame is 0.0.
>
> In order to check there is no problem with my trajectory file,
> I reload the trajectory file to VMD, and type
>
> ---------------------------------------------------------
> set all [atomselect top all]
> set ref [atomselect top "protein and backbone" frame 0]
> set sel [atomselect top "protein and backbone"]
> $all move [measure fit $sel $ref]
> measure rmsd $sel $ref
> ---------------------------------------------------------
>
> and it give the result of '1.1698527336120605'. It proves that nothing
> is wrong with my trajectory file.
>
> The TCL script for analysis RMSD is:
>
> -------------------------------------
> set namdpsf ribuamd.psf
> set namddcd10 ribua_md_60.dcd
>
> source bigdcd.tcl
> set outfile [ open rmsd.dat w ]
>
> proc myrmsd { frame } {
> global mol outfile ref sel all
> $all move [measure fit $sel $ref]
> puts $outfile "$frame [measure rmsd $sel $ref]"
> }
>
>
> set mol [mol new $namdpsf waitfor all]
> set all [atomselect $mol all]
> set ref [atomselect $mol "protein and backbone" frame 0]
> set sel [atomselect $mol "protein and backbone"]
> bigdcd myrmsd $namddcd10
> bigdcd_wait
> close $outfile
> #quit
> -------------------------------------------
>
> Could you please give me some help?
> Thanks in advance!
>
> --
> Jianing Song
> Ph. D. Student
> Institute of Theoretical and Computational Sciences
> Dept. Phys.
> East China Normal University
> 200062
> 3663 North Zhongshan Road
> Shanghai, P. R. China
>
>