From: João Ribeiro (
Date: Thu May 25 2017 - 08:37:59 CDT

Dear Pratik,

to add some more comments to Ashar answer, it would be better for us to
understand the problem if you add more details of your system, like, what
structure did you prepared, how did you prepared and etc.

Other point that I would like to mention is that you can use QwikMD to
prepare your simulation, if you are not familiar with MD simulations.
QwikMD is a VMD plugin and it is already available in the version 1.9.3 ( Follow the tutorial ( and there you can find a
lot of information. Also, you can find more training material in the same
tutorial page.

I hope that this helps



On Wed, May 24, 2017 at 6:49 PM, Ashar Malik <> wrote:

> 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" <>
> wrote:
> 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.

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3000380