AW: About Constraint Failure

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Oct 16 2013 - 00:31:03 CDT

I don't know what was spoken here already, but what's simply about doing
some more minimization steps? You can use the VMD "Namd Plot" plugin to plot
the TOTAL energy from the minimization log file. You should export it to
f.i. xmgrace to be able to zoom into it, as an initial high peak usually
hides the nature of the curve. Check if the TOTAL energy converges to an
almost constant value, if not -> minimize longer. This is the most common
reason for this error to occur and it is and EIFK - error in front of
keyboard ;)

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Kenno Vanommeslaeghe
> Gesendet: Dienstag, 15. Oktober 2013 19:33
> An: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: About Constraint Failure
>
> Your "very popular errors" point to equally popular system preparation
> mistakes. I'm only on this mailinglist to help people with CHARMM force
> field issues. I replied because you posted a message on Sunday
> indicating
> that you were doing potentially scary things with force fields / atom
> types. Consequently, even if you manage to fix your system preparation
> errors, your simulation results may or may not be correct depending on
> what exactly you did with your force field (which is not clear to me).
>
> I assume you have an advisor or senior lab member who works in this
> field
> (if not, you probably shouldn't be trying this). Ask them how to fix
> your
> system preparation errors.
>
>
> On 10/15/2013 05:57 AM, Vidhya Sankar wrote:
> > Dear sir,
> > Thank you for your Previous reply
> > I am running the Namd Simulation After Energy Minimization It shows
> Very
> > Popular error as follows
> >
> > ERROR: Constraint failure in RATTLE algorithm for atom 1242!
> >
> > ERROR: Constraint failure; simulation has become unstable.
> >
> > ERROR: Constraint failure in RATTLE algorithm for atom 1562!
> >
> > ERROR: Constraint failure; simulation has become unstable.
> >
> > ERROR: Constraint failure in RATTLE algorithm for atom 265!
> >
> > ERROR: Constraint failure; simulation has become unstable.
> >
> > ERROR: Exiting prematurely; see error messages above.
> >
> > Then I using VMD To get Namd plot (for total Energy)
> > It Shows the energy Suddenly falls to 7.5e+08 after 150 steps and
> > Suddenly hikes to 1.60e+09 at the end Em (1000steps)
> >
> > How to Solve it ? Which Parameter Should I Adjust ?
> >
> > Should I Diagnosis The Particular atom ? then i How to Diagnosis?

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