Re: cgmd stability

Date: Wed Feb 18 2009 - 20:20:52 CST

Hi Peter:

Thanks for your reply.
I'm using 1-2 exclusions, and the dynamics is indeed stable if I have
no pulling at all. You are also right in the fact that the stability
depends on the pulling velocity. However, it seems to be more stable
when I pull it faster, which does NOT really make that much sense to me.
Can you be more specific about "deforming"? unphysically long bonds?


On Feb 18, 2009, at 6:05 PM, Peter Freddolino wrote:

> Hi Bin,
> can I verify that you're using 1-2 exclusions and not 1-4? RBCG is
> designed to go with 1-2 exclusions, and any other setting can
> certainly
> cause the problems that you're seeing. If that is not the problem, I'd
> recommend looking at your system immediately before you get crashes
> and
> seeing if things are becoming visibly deformed. Have you tried running
> without the applied pulling, or with a slower pulling velocity?
> Peter
> BIN ZHANG wrote:
>> Dear all:
>> I've been experiencing with rbcg using NAMD for a while, and often
>> got
>> the error "FATAL ERROR: Bad global exclusion count!" during the
>> simulation, even with a time step as small as 5 fs. (This could also
>> partially blame the calculation I was doing probably, pulling peptide
>> through membrane)
>> Searching about the list, I found the following reply from peter:
>>> Hi Jiaqi,
>>> it is important to understand the source of the bad global exclusion
>>> count error: Two atoms which should have an exclusion are not on
>>> neighboring patches. This happens a lot in coarse grained systems
>>> because they have such long bonds. What do you have exclude set
>>> to? And
>>> how far apart are your particles?
>>> Peter
>> If this is the case, I wonder would decrease the number of cpus used,
>> or increase the "margin" parameter help in solving the problem? Is
>> there other way to systemically reduce the error occurring?
>> BTW, I do NOT think this error occurs due to bad initial
>> configuration, because it could happen after several ten ns running.
>> Thanks a lot.
>> Bin

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