Re: Mysterious Formation of Solvent Spheres

From: Charles Zhao (
Date: Wed Aug 11 2010 - 18:19:07 CDT

Actually, do you mind describing more the conditions under which tip3p water
has formed droplets in the past? Does it usually have something to do with the
periodic cell or is just something that happens? I have already included my
configuration file. Looking through the temperatures and pressures in the
output log, I don't see anything particularly anomalous, except that the
pressure fluctuates a lot (gpressave swings between +4 and -1) but I gather this
fairly common. The volume and temperatures seem to be as expected...

From: Axel Kohlmeyer <>
To: Charles Zhao <>
Sent: Wed, August 11, 2010 3:23:36 AM
Subject: Re: namd-l: Mysterious Formation of Solvent Spheres


i don't think that there is something mysterious going on.

computer programs are not very smart and only do
what they got told to do (unless they have bugs).
for something that is used as much as NAMD, the chances
are _much_ higher that you didn't tell it what you
wanted it to do. this is also known as the GI-GO principle.

On Wed, Aug 11, 2010 at 2:32 AM, Charles Zhao <> wrote:
> I constructed a group of similar solvated protein systems in periodic box
> boundary conditions using the exact same procedure. Then I ran them all in
> namd 2.7b2 for 10ns using virtually identical configuration files (I
> literally copy/pasted, changed the filenames, and changed the periodic box
> sizes to properly match the system).

please note, that copy-n-paste is a frequent source of errors.
it is very easy to miss a character here or there.

> The problem is, now I have some systems where the solvent congeals into this
> sphere shape (with a few waters flying off into the distance), and others
> where it stays in the proper shape of a box. The only thing I can think of
> is that the water density is somehow too low in the sphere systems. But
> then why is it perfectly fine in the remaining systems? They're all of

who says that it is perfect in the other systems? perhaps they are
just in a metastable configuration. have you calculated the total
density in those systems?

> similar size, differing perhaps by 30 or so angstroms in various dimensions,
> and constructed by the same method. And since when does water in a periodic
> box system, no matter how low the pressure, decide to form a sphere in the
> middle?

water does this since there are three phases: solid, liquid and gaseous.
if your water potential can reproduce those, it can form droplets,
periodic boundaries or not. TIP3P definitely can form droplets.

your description is lacking detail, so it is very difficult to assess
what is going wrong, but it almost looks as if your equilibration
protocol seems to be way off, and that most likely _all_ your
simulation results may be useless. please let us know in more
detail what steps you performed in order to equilibrate your
initial configurations for the production simulations. in what
ensemble were you running when you observed the formation
of the water droplet? nvt, nve, npt?



Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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