Re: AMBER: Separation of a Water molecules

From: Dr. Yong Duan <>
Date: Thu, 13 Nov 2003 00:43:26 -0500 (EST)

It is almost the strangest thing I've ever seen (I do not believe I am the
only one here who feel this way).

As if you are simulating a NVT box with a field gradient (e.g.,
gravity) that drove the water molecular to form a plain surface instead of
bubbles. It appears there is net force applied to the system along
X-direction (horizontal). This force is actually orders of magnitude
greater than the gravity. If this was not the case, it implies a bug. Of
course, this is just my wildest imagination.

Please, check your mdin and make sure ntb=2, ntp=1, and other related
parameters are set correctly. I believe the default values are suitable
for typical calculations.

If this is the case, try increasing your target pressure to 2000-5000 atm.
If this still does not solve the problem, we ineed need to find out where
does this net "X-force" come from.

Good luck!

> > From: "nabe" <>

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Received on Thu Nov 13 2003 - 04:53:01 PST
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