Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry?

From: Pablo Englebienne <>
Date: Thu, 8 Nov 2007 12:44:43 -0500

Thanks German, I tried that (ntc = 3, ntf = 3) but unfortunately I got
a shake error after 0 iterations:

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I then realized that the problem was probably due to having an atom
with a mass of 0; I tried setting to 1 and the problem is solved. The
large K for the bond stretch keeps the bond length at 1A, the Pt is
square planar and the energies are reasonable.

Thanks again!
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501    Fax (514) 398-2382
"Progress is made by lazy men looking for easier ways to do things." -
Robert A. Heinlein
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Received on Sun Nov 11 2007 - 06:07:31 PST
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