From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 23 2007 - 14:54:38 CDT
Please have a look at some of the many previous threads accessible on
the namd mailing list archives about proteins out of water boxes, eg,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5873.html. This
is a fairly common behavior, and probably doesn't indicate a problem,
since the protein's coordinates will not be wrapped until the entire
chain crosses a boundary. As long as your periodic cell is correctly
sized, the system is behaving normally.
Peter
ramya narasimhan wrote:
> Dear Namd Users,
> Iam a new user of NAMD.I tried to do MD of peptide
> with water in NPT ensemble. I used Langevin dynamics to maintain the
> temperature at 300K. I used PBC.My peptide went to the corner of the
> box,then I made some changes according to the tutorial and this time
> peptide went out of the water box.Can anyone point out the error in my
> protocol.I have enclosed my configuration file along with this mail.
>
> Thanks in advance.
> Ramya.L.
>
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