Re: Error while running NPT Simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Oct 16 2008 - 14:07:26 CDT

Hi Navdeep,
does your unit cell contain *1* copy of this hexane derivative or is it
filled with bulk compound? It is unclear from the wording of your
question, and makes a big difference.
Peter

Nd S wrote:
> Hi all
>
> I ran a NPT simulation and the volume of the cell decreased from
> 1,001,290.4628 to 471,602.1941 and after that the simulation crashed
> giving the following error:
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 65000
> WRITING COORDINATES TO DCD FILE AT STEP 65000
> WRITING COORDINATES TO RESTART FILE AT STEP 65000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 65000
> FINISHED WRITING RESTART VELOCITIES
> 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 ran the simulation for 100,000 steps. The unit cells contains only a
> derivative of 1-Hexene. Can you please explain me what happened and
> how I can correct this.
>
> Thanks a lot,
> Navdeep

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