Hi Ying,
The TIP3P water model was parameterized specifically for use with shake,
hence turning off shake for TIP3P will result in the water model no longer
providing satisfactory results.
If you really want to run your solute without shake then you can use the
shakemask variable to only shake the water atoms (you still need a time step
of 1fs or less though). Alternatively you could use a flexible water model
like spcfw.
Good luck,
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Wang,Ying
> Sent: Wednesday, June 18, 2008 1:07 PM
> To: amber.scripps.edu
> Subject: AMBER: tip3p water and shake
>
> Dear all,
> If I perform a simulation in explicit solution, like tip3p
> waterbox, could I turn off shake? because manual say that tip3p
> water like a rigid triangle but if turn off shake the bond length
> involve hydrogen will be changed. So I'm worried about that and
> ask you. Thank you very much!
>
> Best,
>
> Ying
>
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Received on Sun Jun 22 2008 - 06:07:18 PDT
