Re: Mysterious Formation of Solvent Spheres

From: Thomas C. Bishop (
Date: Wed Aug 11 2010 - 13:48:10 CDT

check your log files.. the only way for waters to "fly into empty space" is a
periodic boundary issue...
 1) a wrap on/off problem; one output wraps the waters the other does not s.t.
looks like flying into space... if you "rewrap" the waters the holes should
get filled by the waters from empty space

  2) the periodic b.c. dimensions were wrong (reported volumes will confirm
if some mistake in specifiying system size

 3)the periodic b.c.s were not on s.t. a bubble in vacuum and the waters
really did go into space in this case you won't have a volume reported in the
log file ( at least I think that's the case)

just my $0.000001/2

On Wednesday 11 August 2010 05:23:36 am Axel Kohlmeyer wrote:
> charles,
> 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?
> cheers,
> axel.

   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392

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