From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jun 01 2012 - 14:44:37 CDT
I'm not sure this is possible in an easy way. But also, I doubt it is
needed, why do you want to do this? As Felipe mentioned, you can always
recenter the periodic box around your complex later, since the wrapping or
not wrapping is just a visual thing. If, for instance, you want to measure
some kind of distance between receptor and ligand, you can recenter
afterwards, or you could use the collective variables module to keep track
of things, as it will by default use the shortest path between things.
~Aron
On Fri, Jun 1, 2012 at 3:20 PM, Felipe Merino <felmerino_at_uchile.cl> wrote:
> Hi,
>
>
>
> In principle this is not a NAMD concern. As far as i know that is
> impossible to do "on the fly". In the end the wrap command is just to
> mantain the original for of the cell on the output. If you wat you
> molecules rejoint you have to post-process the dcd in VMD. the command is
> something like pbc wrap -all -centersel yourComplex. The you can further
> repair any weird thing due to crossing the cell with pbc join (I don't
> remember exactly the command here). Check the pbcTools manual for VMD.
>
> Regards
>
>
>
> Felipe
>
> ----Mensaje original----
> De: M.Porrini_at_ed.ac.uk
> Fecha: 01-jun-2012 14:52
> Para: "Namd Mailing List"<namd-l_at_ks.uiuc.edu>
> Asunto: namd-l: issue with solute that splits
>
>
> Dear all,
>
> I would like my solute (made up of a dimeric protein plus a ligand)
> to be translated as a whole to the other side of the cell, when it
> crosses the periodic
> boundary.
>
> As far as I understood, activating the keyword "wrapAll on" in the
> NAMD config file,
> all the molecules (which are composed by contiguous atoms) in my system
> will do that, but I would like my complex (monomer + monomer + ligand)
> to do that as a whole.
> Let's say when the center of mass of my complex crosses the boundaries
> of the box,
> it will be translated on the other side of the cell.
>
> Any hint on how I can accomplish this would be really appreciated.
>
> Many thanks in advance.
>
> Best,
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini_at_ed.ac.uk
> mozz76_at_gmail.com
> maxp_at_iesl.forth.gr
>
>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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