From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Oct 20 2014 - 01:14:02 CDT
The pbx tools directly can’t wrap in only selected dimensions. But you can wrap by centering a particular selection of your system. Example:
In vmd : pbc wrap -all –compound res –center com –centersel “your sel for membrane”
To finally keep it from moving use the RMSD Trajectory Tool and “Align” using the same selection as above. Maybe that helps. You can write a new DCD using VMD Main->File->Save Coordinates.
If you really need to wrap in only two dimensions, you would need to write a TCL script for that. This wouldn’t be difficult.
Von: Maria Bykhovskaia [mailto:mb.ucdelcaribe_at_gmail.com]
Gesendet: Freitag, 17. Oktober 2014 15:44
An: Norman Geist
Betreff: Re: namd-l: wrapping in two dimensions
Thanks. I looked at the periodic representation, but I'd like to save the periodic image in pdb to be used by other applications, and I don't see any way to do this.
Well, it's vmd question only if vmd can do it, and I'm not sure yet if it can. I thought about an option of reading a dcd file with namd, changing the cell origin position, and then rewriting dcd. Would that be doable?
On Fri, Oct 17, 2014 at 4:21 AM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
Why not simply have a look at the „periodic” tab for representations? ;)
Create a representation for the membrane only and show its periodic Z image. So you can see both interacting sites at a time.
BTW this is a vmd question, isn’t it !?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Maria Bykhovskaia
Gesendet: Donnerstag, 16. Oktober 2014 22:34
Betreff: namd-l: wrapping in two dimensions
Is it possible to wrap around a part of the system in one or two dimensions?
Here is the problem:
I model a protein on the top of the lipid bilayer. I have periodic conditions with flexible cell. The membrane stays in place, the protein moves around. At some frames it moves laterally, and part of the protein shifts out of the cell. However, I can see that the protein actually should interact with the mirror image of the membrane, since it is on the same level with the membrane at Z ax (the membrane is on XY plane). I want to visualize the interaction of the protein with the membrane continuation (mirror image).
I have aligned and recentered the system around the protein. When I wrap around the whole thing, the membrane image is on the top of the protein, and that does not help.
Is there any way I can wrap the membrane laterally, over XY (or just over X) without changing its Z position?
Will greatly appreciate any ideas.
-- Maria Bykhovskaia Professor and Chair, Neuroscience Department Director, Specialized Neuroscience Research Program Universidad Central del Caribe Bayamon, Puerto Rico <http://maria.ucdelcaribe.org/> http://maria.ucdelcaribe.org <http://neuro.ucdelcaribe.org/> http://neuro.ucdelcaribe.org http://SNRP.uccaribe.net _____ <http://www.avast.com/> Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus <http://www.avast.com/> Schutz ist aktiv. -- Maria Bykhovskaia Professor and Chair, Neuroscience Department Director, Specialized Neuroscience Research Program Universidad Central del Caribe Bayamon, Puerto Rico <http://maria.ucdelcaribe.org/> http://maria.ucdelcaribe.org <http://neuro.ucdelcaribe.org/> http://neuro.ucdelcaribe.org http://SNRP.uccaribe.net --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com
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