Re: Controlling water diffusion

From: Peter Freddolino (
Date: Thu Jul 16 2015 - 21:54:49 CDT

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.

> 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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