RE: Re: Help !!! ERROR: Atoms mooving too fast

From: Jeff Wereszczynski (
Date: Tue Apr 03 2007 - 18:02:33 CDT

Hi Andrea,

I had a problem like this. What I was doing was minimizing the structure
and then running dynamics (with a flexible cell) in the same input script,
and this caused the system to crash with this fatal error. To fix it I just
ran the minimization and heating (with a fixed cell size) in one input
script, and then in a separate input script I ran the dynamics with the
flexible cell. I don't know why this worked, maybe some sort of memory
issue, but it did and I have yet to see that problem again.

Hope that helps,

-----Original Message-----
From: [] On Behalf
Of Andrea Diaz
Sent: Tuesday, April 03, 2007 3:47 PM
Subject: RE:Re: namd-l: Help !!! ERROR: Atoms mooving too fast


I have been running the equilibration again, minimizing for 5000 steps and
increasing the pairlistdist parameter from 18.5 to 30 ( my cut off is 14 ),
it didn't work. Now I am getting this error:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

I am giving the dimensions to the cell vectors using VMD, I used the minmax
command and I assigned the value of the length of the box that I measure
from vmd to the configuration file. Is this wrong ?

I am using NPT simulation, for that reason I don't believe that disable the
UseFlexibleCell parameter was a good solution.

Thanks a lot .. I will be waiting for your suggestions


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