Namd grid forces -distance between molecule and surface

From: Mohan maruthi sena (
Date: Fri Jun 27 2014 - 05:20:29 CDT

Hi all,
            I have a cubic box containing 256 hexane molecules. The hexane
molecules are placed on surface in xy plane. I use Namd grid forces mimic
the surface. I have got a surface.dx file. My questions are as follows,

1) How to make sure that surface is present in xy plane ?
2) How to calculate the distance between surface and nearest atom in hexane?

Thanks & Regards,

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