AW: Coarse-Grained fatal error!

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri May 03 2013 - 00:25:54 CDT

No, it shouldn't be the size of the box. Was this a NPT run? Have you used
fixed atom or restraints? What timesteps do you use?

 

We need to clarify the above questions first, to make reliable suggestions
what might be happening.

 

Regards

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Fugui
Gesendet: Donnerstag, 2. Mai 2013 14:49
An: NAMD
Betreff: namd-l: Coarse-Grained fatal error!

 

Hi everybody,

I was running a coarse grained MD, and it stoped after 537200 steps, and
the error is:

ERROR: Margin is too small for 3 atoms during timestep 537309.

ERROR: Incorrect nonbonded forces and energies may be calculated!

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.

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.

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.

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.

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.

So it means i need to increase the size of the box, is it right?

BW

Fugui

 

 

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