> I ran a MD simulation with pmemd.cuda for a pure water box of 1994 water
> molecules with SHAKE algorithm turned on. But when I checked the bond
> length and H-O-H angle of the water molecules, they still fluctuated for
> around 0.1~0.2. In my case I need to make the water molecule perfectly
> rigid.
If the O-H or O-O bond length fluctuates by 0.1-0.2 Angstroms, then this
is a real problem as there would be no energy conservation, likely the
integrator would fail, etc...
I just checked one of my simulations and see that the fluctuations
(standard deviation) of O-H or H1-H2 bond lengths are ~0.0004 A and
~0.04 degrees for the H1-O-H2 angle for a salt solution that was run with a
SHAKE tolerance of 0.00001, so how are you estimating the ranges?
If I plot the time dependent bond/angle length, the range of values is
approximately +/-0.0015 A or +/-0.1 degree.
If you want it to be "more" rigid, increase the SHAKE tolerance. However,
it is numerically difficult (effectively infinitely small tolerance) to
get it completely rigid.
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 10 2013 - 12:30:03 PDT
