Re: namd cvs compilation

From: Peter Freddolino (
Date: Mon Dec 01 2008 - 13:14:10 CST

Hi Bin,
at this point you may need to inspect your system to make sure it is
properly solvated, that you don't have any abnormally long bonds, and so
on. You might want to raise the margin from 5 to 10 during minimization.
Also, I'd note that it's not generally considered safe to use multiple
timestepping with the rbcg model, and that you probably ought to define
a switching distance.

BIN ZHANG wrote:
> Hi, Peter:
> Thanks for your reply.
> I have tried using 1-2 exclusions, though now I'm not getting
> the error immediately, it still occurs at 85 steps.
> :
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
> Another thing might deserve to mention is that, now I can start
> to run MD, which was not possible before. But the MD will die with an
> error:
> ERROR: Atom 559 velocity is 588.344 1129.11 541.899 (limit is 800)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
> I also attached my current configuration file in case you are
> interested.
> BTW, I also added these 2 parameters to the rbcg-2007.par file:
> Nxg Nxx Nxg 2.988 92
> Nxg Nxg Nxg 2.988 92
> Is it safe to do this?
> Thanks a lot.
> Bin

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