Re: Controlling water diffusion

From: Evandro Semighini (
Date: Fri Jul 17 2015 - 07:44:36 CDT

Hello Peter,

Thank you !

I really thought this strange, because using CHARMM FF this two things
never happened to me or my co-workers, and because PME was always set in my
simulations, so, I was expecting that the part of the protein that gone out
of the box would be "teleported" to the other side of the system. I always
imagined how it will mess up RMSD measurements.

Yes, I saw the deformations on the water box you said, and I imagined it
happened due to the empty space left by the protein at that volume.

So, it's more a issue with visualization of the system, since I am using
PME, and the protein goes trough the MD normally?
Thank you for the tip of pbctools and periodic images, I saw it yesterday
was waiting the "out of box" run finish to have more material to work with.

Thank you again !

2015-07-16 23:54 GMT-03:00 Peter Freddolino <>:

> Hi Evandro,
> The key here is that you’re simulating a periodic system. You don’t have
> just one box, but an infinite number of identical boxes tiled through
> space. So when your waters appear to go out of the box when wrap is off,
> they’ve just gone into the next periodic copy over (but it is replaced by a
> copy coming in through the other side, so the contents of your unit cell
> are constant). When you have wrap on, your protein may appear to stick out
> of the box because it hasn’t moved far enough to be wrapped. You should see
> a complementary gap in the water on the opposite side of the system where
> it is occupying space. Viewing your system with the help of the pbctools
> plugin, or with periodic images turned on (in the ‘periodic’ tab of the
> graphical representations menu), can help to see what the system really
> looks like.
> Best,
> Peter
> > On Jul 16, 2015, at 3:21 PM, Evandro Semighini <>
> wrote:
> >
> > Hello,
> >
> > I am running NAMD using AMBER Force Field and I am facing a issue with
> the water box.
> >
> > I measured the water vectors and size with VMD and configured the
> periodic boundary conditions as described at the tutorials, and ran a
> simulation, without defining PMEGridSize and using wrap comands.
> > The simulation goes well, except that the water molecules diffuses a lot
> away from the box, they seems to evaporate.
> >
> > I used then the wrapWater and wrapAll comands and things got more
> strange, as the protein is entirely removed from the water box after energy
> minimization, but the MD runs ok after that.
> >
> > I checked the data from the cell vectors and center, as well as the
> coordinate files and the numbers are within the expected values.
> >
> > The minimization seems to reset the coordinates of the protein.
> >
> > Can anyone, please, point me where I am missing ?
> >
> > Thank you,
> > Evandro

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