On Tue, Feb 05, 2013, Jonathan Saboury wrote:
> I am currently simulating a molecule in explicit water with OpenMM with
> prmtop and inpcrd created by AMBER form a pdb. I'm having a problem
> simulating the molecule for a long time because the molecule of interest
> eventually reaches the edge of the box of water and is partially out, which
> I would assume would affect the simulation.
This sounds like an imaging issue; simplest check is to use the autoimage
command in cpptraj to re-pack the molecules into a continguous unit cell.
Note that in periodic boundary conditions there is no "edge" of the box of
water; everything is replicated periodically in all dimensions.
...good luck....dac
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Received on Wed Feb 06 2013 - 05:00:03 PST
