Re: cgmd stability

From: Peter Freddolino (
Date: Thu Feb 19 2009 - 06:46:40 CST

BIN ZHANG wrote:
> Why would this matter? I thought SMD should have nothing to do with
> the model I use (whether all-atom or coarse-grained).
In principal you're correct, but in practice this does mean that no one
has done much testing of what pulling rates can be reasonably used
without breaking the model.
>> Are you pulling by one bead or the
>> center of mass of several? Also, do the crashes happen consistently
>> around the same time if you go repeat the crashed run?
> What do you mean by repeat? I did several simulation from the same
> configuration, but with different random numbers, and they do NOT
> crash at the same time. But I didn't really test "same configuration,
> same random number".
I had assumed (maybe incorrectly) that your run was broken up into
several segments, and was just wondering if you tried rerunning the last
of them whether the crash happened at roughly the same time. The reason
I'm wondering is what you really ought to do is a run where, in the time
range where you expect it to crash, you write energies and a dcd file
every step so that you can see what is breaking. The easiest way to do
this is probably to restart from the latest set of restart files before
the crash, with the more frequent output; I was just wondering whether
the crash happens at roughly the same time when you try this. In any
case, that'd be my recommendation for figuring out what is going on,
since I've never seen behavior like what you're describing except at the
very beginning of a CG simulation.

> Than

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