Re: cgmd stability

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Feb 18 2009 - 23:41:27 CST

Well, unphysically long bonds, or the membrane bending, or the protein
deforming. Please keep in mind that people haven't really done a whole
lot of SMD work using this 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?
Peter

BIN ZHANG wrote:
> 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?
>
> Best,
> Bin
>
>
> 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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> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.

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