From: Ashar Malik (
Date: Wed May 24 2017 - 20:49:05 CDT

Hi Pratik,

Please use the NAMD list for Simulation related questions.

Secondly, I don't think pockets inside the protein are filled by the
solvation process. Solvation is usually around the protein only and not
inside, unless the pockets are big enough. The methods of solvation that I
am aware of puts the protein in a water box and deletes overlapping atoms
which are within a distance cutoff from protein atoms. Of this was used
then depending on how big the pockets are and how big was your cutoff and
how you chose to solvate will determine if the space inside (assuming it's
big enough ) will get filled. You can check this by checking water
coordinates within minmax of protein.

On May 25, 2017 07:54, "Pratik Narain Srivastava" <>

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.