From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Tue Nov 20 2007 - 11:35:51 CST
I think that when you integrate the slow variables you should use a much
smaller timestep than you must be doing. If you want to use a large
timestep, then you can do inner iterations -- e.g. advance for dt/10,
run short MD to equilibrate, advance for another dt/10, equilibrate,
etc., until you get to t+dt.
I cannot think of any method that will tell you whether your coarse time
step is too large
On Tue, 2007-11-20 at 11:10 -0500, Yinglong Miao wrote:
> 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?
> 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