From: Peter Freddolino (
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, 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.

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.
> ------------------------------------------------------------------------
> Now you can chat without downloading messenger. Click here
> <*>
> to know how.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:24 CST