Re: cgmd stability

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Feb 19 2009 - 11:25:41 CST

Thanks for your suggestions.
I would give it another shot, and let you know if I found anything new.

Best,
Bin

On Feb 19, 2009, at 4:46 AM, Peter Freddolino wrote:

>
>
> 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.
>
> Best,
> Peter
>>
>> Than
>>

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