Re: peptide out of the water-box

From: Jim Phillips (
Date: Thu Aug 25 2005 - 18:08:52 CDT

If you're seeing lines like this in the output:

Info: PERIODIC CELL BASIS 1 108.861 0 0
Info: PERIODIC CELL BASIS 2 0 108.861 0
Info: PERIODIC CELL BASIS 3 0 0 77.758

but you don't see a hole in the other side of the water, make sure that
your periodic cell is the same size as your water. You may be simulating
a bubble of water in a large vacuum. As a simple check, try setting
cellOrigin to the center of mass of your peptide and continuing the
simulation (you can do this in the .xsc file if you're using it, it's the
o_x, o_y, o_z values). If you have wrapping enabled (wrapWater or
wrapAll) your output coordinates should then have the peptide in the
center of the cell.


On Mon, 22 Aug 2005, Navratna Vajpai wrote:

> Dear NAMD users..
> Hi.
> 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 parameters.
> Thanks in advance for any kind help
> Best regards
> nav
> *****************************************************************
> Navratna Vajpai Ph.D student in Prof. Stephan Grzesiek's group
> NMR in Strukturbiologie,
> Abt. Strukturbiologie & Biophysik,
> Biozentrum,
> CH-4056, Basel,
> Switzerland
> Phone - 0041 76 375 2003(M)
> 0041 61 267 2097(O)

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