Re: Re: NAMD: Exiting Prematurely

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
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.

Regards,
         Jeff

======================================================================
Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
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
http://potoff1.eng.wayne.edu
======================================================================

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