Re: problem regarding rattle algorithm

From: Francesco Oteri (
Date: Fri Dec 31 2010 - 03:57:29 CST

Regarding the first problem, you should check if the atom 11181 contacts
protein. If this is the case, remove it. If this is not the problem, try
to use 1fs (or smaller) as timestep and a lower temperature (100K or

The second problem, in my opinion, is due to some error in the
submission but it is difficult to say what is the error whitout any
knowledge of the queue system, submission script, etc.etc.

Il 31/12/2010 09:29, Prathit Chatterjee ha scritto:
> Hello NAMD Experts,
> I am facing a problem running an NPT simulation of
> a protein in a lipid bilayer. After minimization, when I am trying to
> run an NPT simulation, I find that the simulation crashes giving the
> error message "Constraint Failure in The Rattle Algorithm For Atom
> 11181 (or may be some other number, which are in the lipid bilayer). I
> even tried to constrain the bilayer and equliibrate the solvents but
> it is of no help. Please help me in this regard.
> Also, there is a problem. In our clusters, if we
> submit a job with NAMD for more than 1 node, it does not use the 2nd
> and/or the other nodes. The nodes remain vacant/unoccupied by the
> respective job.
> Can any one of you assist me?
> with regards
> Prathit Chatterjee

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