AW: RE: Wrapping

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Sep 17 2012 - 01:08:36 CDT

What's the problem with snap1? If you don't like the overlong bonds, you
should use "-compound res" and center what you want to have in the center of
the box to not be sliced by the box borders "-center com -centersel
protein". This will remove the overlong bonds. If you don't use "-sel" while
wrapping, the "wrap" command will by default use "all" so it's just not
possible that you don't have everything in the box after wrapping. Also your
pictures doesn't show a problem, especially no atoms that are outside the
pb. So what u need is I guess:

pbc wrap -all -center com -centersel protein -compound res -sel all

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: Buddhadev Maiti [mailto:bmaiti_at_gsu.edu]
> Gesendet: Donnerstag, 13. September 2012 18:35
> An: Norman Geist; 'Cruz-Chu Eduardo Roberto'
> Cc: Namd Mailing List
> Betreff: RE: namd-l: RE: Wrapping
>
> Dear NAMD Users,
>
> Thank you very much for your reply. After using those commands:
>
> pbc wrap -all
>
> or
>
> # wrap 100 times
> set i 0;
> while { $i < 100 } {
> pbc wrap;
> incr i;
> puts "working on wrap number $i";
> }
>
> I was getting snap1.jpg
>
> Then I used the command:
>
> pbc join res -border 3 -all
>
> I was getting snap2.jpg
>
> Therefore after wrapping, I didn't get everything including protein,
> lipids, ions and water in the same box with perfectly. I am sending the
> snapshots as attachment. Please let me know your opnion.
>
> Have a nice day,
> Thanks again,
> Maiti
>
>
>
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Norman Geist [norman.geist_at_uni-greifswald.de]
> Sent: Monday, September 10, 2012 3:27 AM
> To: 'Cruz-Chu Eduardo Roberto'
> Cc: Namd Mailing List
> Subject: AW: namd-l: RE: Wrapping
>
> Hi,
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Cruz-Chu Eduardo Roberto
> > Gesendet: Samstag, 8. September 2012 21:15
> > An: Buddhadev Maiti; namd-l_at_ks.uiuc.edu
> > Betreff: namd-l: RE: Wrapping
> >
> > # wrap 100 times
> > set i 0;
> >
> > while { $i < 100 } {
> > pbc wrap;
> > incr i;
> > puts "working on wrap number $i";
> > }
> >
> > ________________________________________
> > From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf
> of
> > Buddhadev Maiti [bmaiti_at_gsu.edu]
> > Sent: Saturday, September 08, 2012 5:35 AM
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: Wrapping
> >
> > Dear NAMD Users,
> >
> > Some atoms must be wrapped multiple time to bring back to the
> original
> > box from the periodic box. The command pbc/wrap/unwrap worked for
>
> OMG since when?? One single wrap will bring the atom back to its
> position in the box no matter how many boxes it is away.
> What you maybe mean, is that you have to do the wrapping for all
> frames, what would be done with "wrap -all".
>
> Norman Geist
>
> > single wrapping but not for multiple wrapping. Could you please give
> > some idea about multiple wrapping specially for water molecules which
> > are far away from the original box and it will be great help for me.
> >
> > Have a nice weekend,
> > Thanks,
> > Maiti
>
>
>

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