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From: Pratik Narain Srivastava (pratik.narain_at_gmail.com)
Date: Wed May 24 2017 - 14:36:45 CDT

I am very new to molecular dynamics. I am trying to simulate a PDB crystal
structure. After running a minimization of 25000 steps, I want to run a
small 100ps equilibration on water only by keeping the protein fixed. After
about 10000 steps of this run I get "Atoms moving too fast" error. What can
I do for it? Also if I delete the waters already present in the structure,
does the waterbox fills up the created space? Please answer these questions
and please point me to some basic literature on MD simulations.