On Sun, Jun 15, 2014, newamber list wrote:
> command: solvateoct hex20 TIP3PBOX 12.0
Note that this command is only intended to give a *very rough* starting
structure for further simulation. The number of water molecules chosen for a
given box size (or buffer size) will be very different from what you will get
after equilibration: the number of waters will stay the same (of course), but
the size of the box will change a lot.
If you choose the same number of waters in Gromacs and Amber, and simulate to
equilibrium at some temperature, you should get the same average properties
(such as density). In Amber, at least, the equilibrated density will be very
different than the initial density. No one in the Amber community has not
(yet) felt a big need to improve the initial guess that LEaP provides.
....dac
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Received on Sun Jun 15 2014 - 09:00:02 PDT
