basic pdb file run with namd and vmd

From: Kayode Karunwi (
Date: Wed May 23 2007 - 16:05:01 CDT

Hi everyone,

I'm new to using namd and tried practicing on some small pdb file, alanine.
This is most likely easy for everyone on this forum.

How do you solvate this molecule and optimize it's energy so it's enclosed
in a water sphere? Attached are the files I modified but feel free to start
with the original pdb file, run through and send back to me at

Thanks in anticipation of your help.


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