[gmx-users] query regarding self-assembly process

jagannath mondal jmondal2004 at yahoo.co.in
Sat Jun 16 03:55:02 CEST 2007

Dear gromacs users,
     I am trying simulate self-assembly of protein on
gold surface. To get an idea, I was looking for
various literatures which this kind of self-assembly.
Many of them reports that they used periodic boundary
condition in X and Y diection(gold-surface is in one
extreme of z direction) and then used a repulsive(
reflecting) wall opposite to the gold surface.
 But, I was wondering if some one can explain  the
algorithm for  how to create wall which will be
repulsive as well as reflective.
thanks in advance,

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