AMBER Archive (2007)

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

From: Pablo Englebienne (pablo.englebienne_at_mcgill.ca)
Date: Thu Nov 08 2007 - 11:44:43 CST

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

--[mdout]--
     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.
--[mdout]--

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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