From: Werner Crous (crous.werner_at_gmail.com)
Date: Thu Jun 02 2011 - 04:05:41 CDT
Hi Johan
Thank you. I tried to use PBCTools. I specified a variable of the fragments
I would like to keep together. I then used pbc join res -ref $keeptogether
and then pbc unwrap. I hope I did it correctly. My substrate is now in the
correct position for most of my frames. there are some where is is still
somewhat away. The water molecules are smeared.
Werner
On Wed, Jun 1, 2011 at 7:19 PM, johan strumpfer <johan.ks.uiuc_at_gmail.com>wrote:
> HI Werner,
>
> This is indeed just an imaging issue. To re-wrap the output it is easiest
> to use the PBCtools plugin in VMD. You can then wrap the resulting
> output either by segment or by residue (see the documentation:
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/). As far as I know,
> namd wrap's dcd output by residue if you specify wrapAll, wrapNearest
> or wrapWater (see http://www.ks.uiuc.edu/Research/namd/2.8/ug/node33.html
> ).
>
> The cut-off that you are referring to I presume is the charmm CUTIM
> parameter? If I remember correctly, this is used to set the maximum
> distance for generating the pairlist. The equivalent parameter in namd
> is pairlistdist. See
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node39.html for more info.
>
> Groete,
> Johan
>
>
> > On Wed, Jun 1, 2011 at 6:09 AM, Werner Crous <crous.werner_at_gmail.com>
> wrote:
> >> Dear NAMD-users
> >>
> >> I have a problem with imaging in NAMD. I used a truncated octahedron
> within
> >> the NVT ensemble. What happened was that after 12ns the protein only
> >> partially moved out of the truncated octahedron, but my one substrate
> was
> >> imaged right to the other side of the box. This then looks as if the
> >> substrate moved out of the protein, but I assume it is just the imaging.
> The
> >> susbstrate is imaged differently to the protein. As a CHARMM user, I
> know
> >> that one can specify if you want the imaging to happen by segment or by
> >> residue, but in NAMD I am not aware of such options. How does imaging
> work
> >> in NAMD for a TOH and what is the cutoff for the minimum imaging
> convention?
> >>
> >> Thank you in anticipation.
> >>
> >> Best regards
> >> Werner
> >>
> >>
> >>
> >> --
> >> Werner Crous
> >> Scientific Computing Research Unit
> >> University of Cape Town
> >> Rondebosch 7701
> >> South Africa
> >> Phone: +27 21 650 2530 (O)
> >> Fax: +27 21 686 4333
> >> http://scru.uct.ac.za
> >> http://scientificomputing.com
> >>
> >
>
-- Werner Crous Scientific Computing Research Unit University of Cape Town Rondebosch 7701 South Africa Phone: +27 21 650 2530 (O) Fax: +27 21 686 4333 http://scru.uct.ac.za http://scientificomputing.com
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