Re: Re: NAMD: Exiting Prematurely

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Aug 15 2007 - 20:20:42 CDT

Vaithee,

Thanks.. thats exactly what I did. And seems to be working for now!

Cheers,

Arun

On 8/15/07, Subramanian Vaitheeswaran <vaithee_at_umd.edu> wrote:
>
> 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
> > **********************************************
>

-- 
***********************************************
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
**********************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:06 CST