From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 23 2007 - 18:20:52 CDT
D'oh, I mean, geometric center, not center of mass.
::looks around for a mountain dew::
Peter Freddolino wrote:
> ::checks::
> 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)
> Thanks,
> Peter
>
> 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,
>>> 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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>>>>
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