Periodic Boundary Conditions

From: Per Jr. Greisen (greisen_at_binf.ku.dk)
Date: Mon Mar 26 2007 - 02:26:19 CDT

Hi,

I have applied periodic boundary condition to a md simulation. I use the
following commands in order to get the values for the PBC

set everyone [atomselect top all]
measure minmax $everyone
measure center $everyone

{-40.5429992676 -40.0960006714 -55.2290000916}
{23.1319999695 25.5699996948 53.1780014038}

and with the center of the protein as
-11.4283914566 -9.76103401184 -0.764146029949

I set the parameter
cellOrigin -11.43 -9.76 -0.76

and the basis vector as the nummerical sum
cellBasisVector1 63.67
etc..

When I display the md simulation - it start out nice as I expect with a
square box but as it continues the waters starts diffusing out. So my
question is - the MD simulation uses the periodic boundary condition but
the vizualisation looks change and can be fixed with the

wrapWater on

Any help or advice appreciated. Thanks in advance

-- 
Best Regards
Per Jr. Greisen

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