From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Tue Nov 20 2007 - 10:10:52 CST
Hi, Peter,
Thanks for your reply!
I read both the trouble shooting webpage you referred to and the user
guide regarding the errors. I also knew what's wrong when I looked at
the ouput trajectory of my simulations. There were unreasonable
stretched bonds and angles in the structure. This cannot be avoided in
my simulations, because I am implementing a method to advance a
macromolecule over long time by using the values of some slow variables
I define and their evolution from short MD runs. As implied by my
method, the slow variables projected over long time may lead to an
unreasonable atomic structure. MY QUESTION IS HOW TO DETERMINE THERE
WILL BE "BAD GLOBAL EXCLUSION COUNT" ERROR FROM THE UNREASONABLE
STRUCTURE IN NAMD. If I know how to do this, I can go back to reduce
the projection time for slow variables until getting a reasonable
structure to continue the simulation with MD run, instead of going
crashed (the default pathway provided by NAMD).
I am also thinking of checking the forces and energies calculated from
the structure, but it seems only forces on several atoms can be
reasonably loaded and I don't know how to load the energies. Do you
have any ideas about this?
Thanks,
Long
Quoting Peter Freddolino <petefred_at_ks.uiuc.edu>:
> Hi Long,
> you can get a feel for what causes these errors at
> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdTroubleshooting.
> The two most important things to do if you're encountering this error
> are make sure your system was sufficiently minimized, and look at your
> trajectory in vmd (possibly writing to the dcd file at every timestep)
> so see if you can see where the instability is occurring.
> Best,
> Peter
>
> Yinglong Miao wrote:
>> Hi, NAMD developers and users,
>>
>> In some of my simulations, I keep getting error messages like "FATAL
>> ERROR: Bad global exclusion count!" and "atoms moving too fast". I am
>> wondering whether there are flag values returned when executing
>> "minimize" and "run". Let's say, when these commands are executed
>> correctly, a flag value of 0 is returned; when above error messages
>> come up, a flag value of -1 is returned so that I can do something to
>> "guide" the simulation according to the flag value instead of just
>> going crashed.
>>
>> If no such flag values returned in NAMD, could anybody tell me how is
>> the error "FATAL ERROR: Bad global exclusion count!" determined? I
>> know it could be due to stretched bonds, too close atoms or other
>> unphysical structure, but how does it work in computation? And how to
>> analyze and evolve the atomic structure to avoid above errors?
>>
>> Any ideas and suggestions will be greatly appreciated!
>>
>> Thanks,
>> Long
>>
>> --
>> Yinglong Miao
>> Ph.D. Candidate
>> Center for Cell and Virus Theory
>> Chemistry Department, Indiana University
>> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
>> 1-812-856-0981(office); http://ylmiao.dict.cn/mypage/
>
-- Yinglong Miao Ph.D. Candidate Center for Cell and Virus Theory Chemistry Department, Indiana University 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405 1-812-856-0981(office); http://ylmiao.dict.cn/mypage/
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