Re: Re:

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Oct 23 2007 - 18:09:50 CDT

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,
> 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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