Re: bigdcd file help

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Jul 05 2011 - 13:19:06 CDT

Here is final working example of rmsd calculatio between frames using bigdcd

source bigdcd.tcl
proc myrmsd { frame } {
 global ref sel all
 $all move [measure fit $sel $ref]
 set fout [open "rmsd.dat" a+]
 puts "$frame: [measure rmsd $sel $ref]"
 puts $fout [format "%f" [measure rmsd $sel $ref]]
 close $fout
}

set mol [mol new solvated_ionised.psf waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
mol addfile solvated_ionised_equil.pdb type pdb waitfor all
bigdcd myrmsd dcd solvated_ionised-01.dcd solvated_ionised_prod-02.dcd
solvated_ionised_prod-03.dcd
bigdcd_wait

Next, I am trying to calculate the distance between two atoms along the
trajectory(in different frame). Does anyone have a tcl script to share that
will be using bigdcd. I will highly appreciate your help. I will upload the
final working tcl script also.

Thank you.

S

On Tue, Jul 5, 2011 at 9:56 AM, snoze pa <snoze.pa_at_gmail.com> wrote:

> 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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