Re: Re: NAMD: Exiting Prematurely

From: Jeffrey J. Potoff (
Date: Wed Aug 15 2007 - 07:10:42 CDT

On Wed, 15 Aug 2007, Arun Krishnan wrote:

> Hi All,
> I tried to restart my simulation from just before it crashed and it seemed
> to run for more steps but ultimately
> crashed with a
> ERROR: Constraint failure in RATTLE algorithm for atom 726!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
> I have taken a look at the archives and the usual suggestions are to
> minimize well before dynamics (I have minimized for upto 3ps), and to heat
> slowly and equilibrate (both of which I have done). I have also checked the
> PMEGrid sizes to see if they are
> ok and it looks like they are. According to someone's rule of thumb, there
> should be one atom for every 10 A^3. I have roughly 39,000 atoms and am
> using 80 as my PMEGridSizeX , y and z which means a total volume of 512,000
> A^3 which seems to be ok according to the rule of thumb.
> Do I need to minimize the system again after heating to 500K? That is,
> minimizing just before the production run at 500K? If so how can I do that?
> When I tried to minimize using my files from the equilibration at 500K, it
> kept taking the temperature as 0 and not 500. Or am I missing something? Any
> help will be much appreciated.

Dear Arun,
         Try using a smaller timestep, such as 1.0 fs (or even 0.5 fs)
until the system is equilibrated.


Jeffrey J. Potoff
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)578-5815

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