Re: Re: NAMD: Exiting Prematurely

From: Jason O'Young (
Date: Wed Aug 15 2007 - 11:37:22 CDT

Hi Arun,

Which forcefield and exclusion policy are you using? I used to get
errors like this until I changed my exclusion policy to 1-3.


On 15-Aug-07, at 1:58 AM, 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.
> Cheers,
> Arun
> On 8/15/07, Arun Krishnan <> wrote:
> Dear All,
> I seem to be running across this weird error. I am trying to unfold
> a small protein. I use the following protocol:
> a) energy minimization of protein + water box
> b) heat to 300K
> c) equilibration for 50ps
> d) Production run for 1ns
> e) Heat to 500K
> f) equilibrate
> g) production run
> All the steps from a-f seem to go fine. I followed the temperature/
> pressure/energy profiles for each step
> and they seem to be fine. However for step (g), the program ends
> abruptly with an "Exiting Prematurely"
> message. That's it.. no other error messages. This happens about
> 2ps into the simulation. I am using an NVT
> ensemble.. I checked the temperature/volume/pressure/energy and all
> are stable. There are no sudden drops
> of any sort.. The only sudden change I found was during stage (f)
> where the total energy during the equilibrate stage
> at 500K rose from -71000 to -66500 or thereabouts and then remained
> stable.
> I also checked the DCD file for the production run at 500K and I
> don't see anything out of the ordinary. The protein
> is still well within the waterbox. Am at a loss to understand what
> could be causing the sudden crash. Is there a way
> to find out more about what caused the premature exit?
> Thanks,
> Arun
> --
> ***********************************************
> Arun Krishnan, Ph.D,
> Assistant Professor,
> Institute for Advanced Biosciences,
> Keio University,
> Center Building,
> Tsuruoka, Yamagata 997-0035
> Japan
> Phone: +81 (0)235-29-0824
> Email:
> URL:
> **********************************************

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