Re: cell origin problem

From: Haleh Abdizadeh (halehabdi_at_sabanciuniv.edu)
Date: Wed Sep 25 2013 - 14:00:49 CDT

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 <
norman.geist_at_uni-greifswald.de> wrote:

> Nothing to worry about and no need to rerun the simulation.****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Haleh Abdizadeh
> *Gesendet:* Dienstag, 24. September 2013 16:53
> *An:* namd-l_at_ks.uiuc.edu
> *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****
>

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