Re: Re:

From: Peter Freddolino (
Date: Tue Oct 23 2007 - 18:18:22 CDT

Yep, that's correct- thanks for pointing that out.
So, please replace what I said previously with "until the chain's center
of mass crosses a boundary)

David Hardy wrote:
> Hi,
> My understanding is that wrapAll=on will wrap whenever the geometric
> center of the chain of atoms crosses a boundary. (See function
> wrap_coor_int() in Output.C for details.)
> Regards,
> Dave
> On Oct 23, 2007, at 2:54 PM, Peter Freddolino wrote:
>> 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.
>> 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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