Controlling water diffusion

From: Evandro Semighini (
Date: Thu Jul 16 2015 - 14:21:50 CDT


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,

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