Re: Continuing simulation after constraint failure error?

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Thu Aug 06 2009 - 13:17:48 CDT

Hi Sujata, 10000 minimization steps should be enough to converge to
the nearest local minimum within machine precision.

It could be that the initial configuration carries some strain, that
you'll get back as soon as you give temperature and the system leaves
that local minimum.

Try saving the DCD file for the equilibration more often, and look at
what happens.

Giacomo

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 Giacomo Fiorin
   Center for Molecular Modeling at
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On Thu, Aug 6, 2009 at 12:59 PM, Sujata Sovani<sujatas_at_scripps.edu> wrote:
> Hi All,
>
> I did minimization and equilibration for 10000 steps fro a 377 residue protein. But I got the error
> Constraint failure in RATTLE algorithm for atom 3327!
> ERROR: Constraint failure; simulation has become unstable.
>
> I got this for not only atom 3327 but may others, one of the solution given to this problem in the mailing list is to run the minimization longer.
> There could be many other things that could have gone wrong but I want to know that if I want to continue minimization for more steps say 100000 can it be done from the current step (so as to save that much computational time). I am not sure if this is recommended (stuck in a local minima??) but if it is how to change the .conf file to restart the minimization from here??
>
> Thank you.
>
> Regards,
> Sujata
>
>

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