VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Wed Mar 23 2011 - 00:06:00 CDT

Dear Ajasja,

Thank you much for your advice.
Following your suggestion, I change the content of .tcl to:
----------------------------------------------------------------
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
    $sel frame $frame
    $all frame $frame
    $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 "name CA" frame 0]
set sel [atomselect $mol "name CA"]
bigdcd myrmsd $namddcd10
bigdcd_wait
close $outfile
#quit
------------------------------------------------

I add "$sel frame $frame" and "$all frame $frame" to update variable
"all" and "sel", but it turns out
nothing changed. RMSD for each frame is still 0.0.

Would you like to give me some more advice?

Thank you very much!

Jianing

On Mon, 2011-03-21 at 09:36 +0100, Ajasja Ljubetič wrote:
> 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
>
>
>