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From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Apr 13 2010 - 13:56:51 CDT
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You may not be running with constant pressure, which is needed to allow the unit cell to change size.
See also the membrane protein tutorial here: http://www.ks.uiuc.edu/Training/Tutorials/
On Apr 13, 2010, at 5:02 AM, suneyna bansal wrote:
> Dear Sir,
>
> I have generated a 60X60 POPC bilayer patch using VMD and then
> minimised it using NAMD. But every time I am getting dcd file containing gaps
> in their periodic cell unit.
>
> Could you please suggest me some way.
>
> --
> With Best Regards,
>
> Suneyna Bansal
> PhD Scholar
> School of Biological Sciences
> Indian Institute of Technology, Delhi
> Hauz Khaas, New Delhi-16
> 9211609904
>
> http://www.iitd.ac.in/bioschool.html
>
>
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