Periodic boundary conditions

From: Navratna Vajpai (
Date: Mon Aug 08 2005 - 03:34:34 CDT

Dear Users ,,.
I have been trying to do MD simulation of a peptide under the periodic
boundary conditions. But every time i ran the MD i encountered a
similar problem. In-spite of using the Periodic Boundary conditions, my
peptide goes near to one of the corners of the water box (after 1.5ns
approx) with some of the part for few 10's of psec goes out of the
water box. Initially I was thinking that there is some thing wrong with
the parameter input file but after discussing in the mailing list and
optimizing all the parameters I re-ran the MD. But I again encountered
the same thing. What I wanted to ask is whether the virtual water-box
which i could see through VMD, is that the true resemblance of the
water-box or the calculations for my peptide carries on with the same
periodic boundary conditions( as in the beginning) whether it is at
corner or not?
Thanks for any 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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