From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 20 2007 - 11:20:39 CST
> MY QUESTION IS HOW TO DETERMINE THERE WILL BE "BAD GLOBAL EXCLUSION
> COUNT" ERROR FROM THE UNREASONABLE STRUCTURE IN NAMD.
If I recall correctly, bad global exclusion counts will occur when atoms
involved in an excluded interaction (bond/angle/dihedral) are separated
by more than the pairlist distance + margin. You can raise the margin to
mitigate this to some extent, although it will slow down your
simulations. It's probably better to avoid pulling fast enough to cause
this situation to occur.
> 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?
>
The tclforces interface allows you to query the forces on whatever atoms
you want via loadforces. don't know of a similar way to query the
energies conveniently during the simulation; you can do this in
postprocessing by using pairinteractions.
Peter
> 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/
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:34 CST