AW: AW: Coarse-Grained fatal error!

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon May 06 2013 - 01:09:08 CDT

Wow, 30fs? Is this the usual setting for coarse grained timestep? As the default timestep is 1fs for all atom, this might be the problem, someone else doing coarse grained could jump in here. Or the settings you used for the barostat. Try turning it off to see if it works then, if it does, you need to adapt your settings.

 

Norman Geist.

 

Von: Fugui [mailto:theoreticalchem_at_163.com]
Gesendet: Freitag, 3. Mai 2013 09:35
An: Norman Geist
Betreff: Re:AW: namd-l: Coarse-Grained fatal error!

 

Dear Norman,

I used 30fs at the first time, and it died at 537200 step, 20fs at the second time, and it died again at 2540600. So it seems that it works to decrease the timestep.

I used NPT and did not use fixed or restraints.

Thank you!

BW

Fugui

在 2013-05-03 13:25:54,"Norman Geist" <norman.geist_at_uni-greifswald.de> 写道:

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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