From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Aug 15 2007 - 20:23:39 CDT
Thanks Vincent for that detailed email. Right now, changing the time step
seems to have solved the problem for me.
Cheers,
Arun
On 8/16/07, Vincent Kraeutler <vincent_at_kraeutler.net> wrote:
>
> A SHAKE/RATTLE failure is a fairly generic indication that "something
> went wrong" and does not indicate much, other than that the positions
> between timesteps changed too much for the algorithm to remain stable.
> In fact, I've seen it happen spontaneously (once). There are two classes
> of possible causes for this:
>
> a) You're straining the implicit assumptions of the program (e.g. too
> large timestep, temperature or pressure coupling is going haywire, weird
> cutoff/pairlist settings, a bug, or just bad luck).
> b) You're using an interaction function which is too stiff for your
> integrator (e.g. wrong setting for exclusions, too stiff forces for
> restraint potential or angles, bad force-field parameters).
>
> What I think you should do:
> 1. make sure that at the end of your equilibration phase temperature,
> pressure, and box volume are no longer changing rapidly;
> 2. assert that extending the equilibration protocol is numerically
> stable by letting it run for a longer period of time;
> 3. starting from the equilibration protocol, change one input parameter
> at a time, and let it run for 1000 steps. Repeat until you have obtained
> the production protocol.
>
> If you've reached the end of step 3: BINGO. If not: you will have a
> better indication of where the problem lies.
>
> BTW, in the case where I had a "bad luck" SHAKE failure, changing the
> temperature from 300 K to 300.1 K fixed the problem. ;-)
>
> Cheers,
> v.
>
> 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* <krishnan_at_ttck.keio.ac.jp
> > <mailto: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 <mailto:krishnan_at_ttck.keio.ac.jp>
> > URL: http://www.iab.keio.ac.jp/~krishnan
> > <http://www.iab.keio.ac.jp/%7Ekrishnan>
> > **********************************************
>
>
>
>
-- *********************************************** 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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