Namd grid forces -distance between molecule and surface

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

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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,
Mohan

• Next message: Prija Ponnan: "Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326)"
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