On Fri, Aug 02, 2013, Wang Chern Hoe (Dr) wrote:
>
> I did a 10 ns explicit water (octagonal box) PME NPT simulation after
> a 20 ps PME NVE equilibration. I noticed the water molecules expanding
> beyond the initial octagonal box, and remaining as spherical droplet of
> water with the protein molecule in the centre. The volume remains more
> or less constant. Is this normal ?
Sounds like you need to re-image your molecules into a central unit cell.
See the "autoimage" command in cpptraj (or, if you just have a single protein
surrounded by water, the "image" command in ptraj.)
...dac
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Received on Fri Aug 02 2013 - 05:30:03 PDT
