From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Wed Aug 15 2007 - 09:19:21 CDT
Hi Arun,
I have encountered these "Constraint failure in RATTLE algorithm" errors, but my systems are quite different from yours - simple organic molecules in water. I only needed to restart the run; with Langevin dynamics and no random number seed specified, the simulation followed a different trajectory.
Maybe you need to reduce the time step at such a high temperature?
Vaithee
---- Original message ----
>Date: Wed, 15 Aug 2007 14:58:25 +0900
>From: "Arun Krishnan" <krishnan_at_ttck.keio.ac.jp>
>Subject: namd-l: Re: NAMD: Exiting Prematurely
>To: namd-l_at_ks.uiuc.edu
>
> 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 <krishnan_at_ttck.keio.ac.jp>
> 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: krishnan_at_ttck.keio.ac.jp
> URL: http://www.iab.keio.ac.jp/~krishnan
> **********************************************
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