peptide out of the water-box

From: Navratna Vajpai (
Date: Mon Aug 22 2005 - 02:52:11 CDT

Dear NAMD users..
A similar type of question I raised few days before and got a descent
reply from Mr. Blake. I did some literature survey and tried to
understand the PBC. but still one thing which is unclear to me is that
why during the MD simulation the peptide goes outside the water-box
in-spite of the fact that PBC is used. I don't know whether it is just
visually that I am unable to see neighboring water-box, which according
to the PBC literature, are associated with the central water-box. But
then to my understanding there should be some hole in the water-box
from where the peptide slips out into the neighboring box.
Unfortunately I am unable to see anything like this in my set up.
Has any one have any idea that does it makes any difference if the
peptide comes out of the water-box in the calculation of force-field
Thanks in advance for any kind help
Best regards
Navratna Vajpai
Ph.D student in Prof. Stephan Grzesiek's group
NMR in Strukturbiologie,
Abt. Strukturbiologie & Biophysik,
CH-4056, Basel,
Phone - 0041 76 375 2003(M)
                0041 61 267 2097(O)

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