Re: cell origin problem

From: Aron Broom (
Date: Wed Sep 25 2013 - 14:53:19 CDT

yes that is correct. If you want to see it with the protein in the middle
you can use the pbctools plugin commands in VMD.

For instance, in the TKConsole, you could enter the following commands:

pbc unwrap
pbc wrap -centersel "protein" -center com -compound residue -all

I'm not actually confident you need to unwrap it first, but at any rate,
the above will work to shift where the periodic box is, such that you're
protein is now in the middle. It assumes that VMD already has the periodic
box values, which it should have automatically if you're loading an NAMD
DCD trajectory.


On Wed, Sep 25, 2013 at 3:00 PM, Haleh Abdizadeh

> Because of the periodic boundary condition? I mean a small part of protein
> comes out of water box but i suppose it should enter the water box just
> next to it. Am I right?
> On Wed, Sep 25, 2013 at 8:44 AM, Norman Geist <
>> wrote:
>> Nothing to worry about and no need to rerun the simulation.****
>> ** **
>> Norman Geist.****
>> ** **
>> *Von:* [] *Im
>> Auftrag von *Haleh Abdizadeh
>> *Gesendet:* Dienstag, 24. September 2013 16:53
>> *An:*
>> *Betreff:* namd-l: cell origin problem****
>> ** **
>> Dear all,****
>> I have made a mistake in entering cell origin coordinates in restart conf
>> file. When I play the movie of trajectories I do not see any problem in my
>> protein but I am not sure if my results are correct or not. I know cell
>> origin is not the center of mass of the protein but center of the water box
>> so could anyone tell me if it is necessary for me to start the whole
>> simulation again?****
>> Best wishes,****
>> Haleh****

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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