From: Ribi Akbar (ra.ribiakbar_at_gmail.com)
Date: Tue Jun 28 2022 - 04:24:52 CDT
Hello,
Thank you for the reply. I found many symbols that are not understandable.
Could you please give me some explanation?.
Thanks in advance,
Best wishes,
Ribi
On Tue, Jun 28, 2022 at 11:10 AM Bunzeki Kilolo (Mme) <
kilolo.bunzeki_at_polytechnique.edu> wrote:
> Hello Ribi,
>
>
> Try ;
>
> bomlev -5
> wrnlev 5
>
> stream job.str
>
> open unit 10 read card name structure.psf
> read psf xplor card unit 10 append
>
> open unit 4 read card name structure.pdb
> read coord pdb unit 4 resid
>
> open read unform unit 22 name traj.dcd
> trajectory first 22 nunit 1 begin 1 skip 250
>
> set i 1
> set ntot ?nfile
>
> label nextconf
>
> traj read
> open write card unit 12 name traj.conf__at_i.pdb
> write coor pdb unit 12
> close unit 12
> incr i by 1
>
> if @i le @ntot goto nextconf
>
> stop
>
>
> Best,
> Kilolo
>
> ------------------------------
> *De: *"Ribi Akbar" <ra.ribiakbar_at_gmail.com>
> *À: *namd-l_at_ks.uiuc.edu
> *Envoyé: *Mardi 28 Juin 2022 09:49:17
> *Objet: *namd-l: pdb file from a particular configuration
>
> Hi,
> I am currently facing a problem when creating a PDB file from the dcd
> file. Suppose that we have 10000 trajectories, each frame shows a different
> configuration of the system (MD simulation) and we are interested in the
> configuration at frame 5000 (MD simulation), is it possible to do this
> using VMD? Thanks for your attention.
>
> Kind regards,
> Ribi Akbar
>
>
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