VDW energy diverged & VMD functions applied on cluster

From: Simon Kit Sang Chu (simoncks1994_at_gmail.com)
Date: Sat Jul 18 2015 - 16:37:54 CDT

Dear NAMD users,

Since VDW energy diverges right at the beginning, I want to read the energy
with a specific set of atoms to figure out the troubled atoms. I tried to
use "NAMD Energy" on my laptop. However, it seems there is not enough
computing power. Is there anyway to apply these functions on cluster?

Moreover, anyone who has experienced VDW energy diverged before? I believe
there are atoms self-interacting / located at the same location. I did
minimization with 10000 steps and the divergence persists.

Thank you very much.


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