From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 16 2010 - 21:27:25 CST
running an evaporation simulation is not a simple task.
you have to deal with all kinds of finite size issues and
resulting hysteresis effects.
furthermore, you _have_ to have a smaller time step
for the system, in order to run a stable dynamics
in gas phase. please keep in mind that the length
of the time step is limited by the fastest motion
in your system. if you have too large a time step,
it will initially evaporate faster due to the larger
time step, but then atoms will move too fast for
the reneighboring to be able to keep track of it,
which is the most likely explanation for the error
message that you are getting for the scenario
that you are describing.
On Tue, Nov 16, 2010 at 7:32 PM, Jason Richard Mick <dw2413_at_wayne.edu> wrote:
> Hi All,
> I've seen lots of posts on this topic on the NAMD mailing list, but none of the suggestions really seemed to explain why my system is encountering this issue. I've also read this:
> Basically, from what I understand, you may encounter this error if:
> 1. You have hydrogen bonds that overlap the PBCs.
> 2. You have too small a cutoff when minimizing.
> 3. You have coordinates at 0,0,0
> 4. A residue is in multiple chains.
> I have 500 methyl acetate molecules inside a simulation box, and want to run an NPT simulation which I expect to go to the gas phase.
> I've checked my *.pdb file to ensure that #3 doesn't apply. #1 doesn't apply as I don't have hydrogen bonding groups. For #3 I've tried a number of box sizes (50x50x50, 80x80x80, etc.) and bumped my cutoff up very high (30,50, etc.) and I still get this error. #4 isn't the case as I only have one chain ID (A) in my system.
> I would expect my system to be in the gas phase once heated, so I would assume I want to start with a large box size (e.g. 80x80x80) so as to ensure a lower density. I would assume that when heated, the system might initially contract, but then would expand to the gas phase as the heating continues.
> What seems to happen is that if I run a sufficiently large time step (1 or 2 fs), I immediately (and consistently) get:
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> FATAL ERROR: Bad global exclusion count!
> at timestep 0.
> If I bump the timestep size down to 0.5 fs, this error goes away, but my system gets stuck in a meta-stable state, I believe, as it stays at a liquid-like density, when it should be transitioning to vapor (target temp and pressure is 475 K, 25 atm).
> Any ideas on how I can run a larger timestep without getting this error besides those outlined in the troubleshooting guide???
> Has anyone run into this issue??
> Jason R. Mick
> Potoff Group
> Wayne State University
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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