Re: bigdcd file help

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Jul 05 2011 - 09:56:15 CDT

Thank you all for your aupport. I will try it today. if it works then I will
post a clean tcl script in my next email to NAMD.

On Mon, Jul 4, 2011 at 8:52 AM, sajad falsafi <sajad.falsafi_at_yahoo.com>wrote:

> Hi
>
> You can add this command in the script.
>
> >> mol addfile solvated.pdb type pdb waitfor all
>
> proc myrmsd { frame } {
> global ref sel all
> $all move [measure fit $sel $ref]
> puts "$frame: [measure rmsd $sel $ref]"
> }
> set mol [mol new solvated.psf type psf waitfor all]
> mol addfile solvated.pdb type pdb waitfor all
>
> set all [atomselect $mol all]
> set ref [atomselect $mol "name CA" frame 0]
> set sel [atomselect $mol "name CA"]
> bigdcd myrmsd dcd solvated_prod-01.dcd solvated_prod-02.dcd
> solvated_prod-03.dcd
> bigdcd_wait
> quit
>
>
> Hope this helps you
> Sajad & Zahra
>
> ------------------------------
> *From:* "Cosseddu, Salvatore" <S.M.Cosseddu_at_warwick.ac.uk>
> *To:* snoze pa <snoze.pa_at_gmail.com>; namd-l_at_ks.uiuc.edu
> *Sent:* Mon, July 4, 2011 1:41:55 PM
> *Subject:* RE: namd-l: bigdcd file help
>
> I'm not an expert on bigdcd. But, because you are reading and removing from
> memory the coordinate file, you are likely losing frame 0 coordinates.
>
> try to load with the psf a pdb file or add something like
> animate read dcd solvated_prod-01.dcd beg 0 end 0
> after loading psf.
>
> If I said something wrong please forgive me!
>
> Regards
> Tanti auguri di buona indipendenza
>
> --
>
> Salvatore Cosseddu
> PhD student
>
> Centre for Scientific Computing and School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
>
> email: S.M.Cosseddu_at_warwick.ac.uk
>
>
>
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu on behalf of snoze pa
> Sent: Mon 04/07/2011 07:29
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: bigdcd file help
>
> Dear NamD users,
>
> I am trying to calculate rmsd from my dcd files. the namd rmsd tcl script
> is
> working fine. Unfortunately, My system size is big and I have multiple dcd
> file for 1ns each.
>
> I am trying big dcd file to get rmsd but somehow it is not working. Here is
> my script
>
> proc myrmsd { frame } {
> global ref sel all
> $all move [measure fit $sel $ref]
> puts "$frame: [measure rmsd $sel $ref]"
> }
> set mol [mol new solvated.psf type psf waitfor all]
> set all [atomselect $mol all]
> set ref [atomselect $mol "name CA" frame 0]
> set sel [atomselect $mol "name CA"]
> bigdcd myrmsd dcd solvated_prod-01.dcd solvated_prod-02.dcd
> solvated_prod-03.dcd
> bigdcd_wait
> quit
>
>
> I will highly appreciate your help.
> Thank you,
> S
>
> ps: Wish you all Happy 4th of July.
>
>

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