Re: problems-periodic cell

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Tue Jan 01 2008 - 12:23:25 CST

Jose,

You can potentially get by this by adding

margin 1.0

to you *.conf file. I continue to increase this number until I no
longer receive this message.

Best

Chris

On Jan 1, 2008, at 10:30 AM, jose correa wrote:

> Dear all
> I am running a NAMD simulacion, but the program yield this message:
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> 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.
> Stack Traceback:
> [0] _ZN9HomePatch14positionsReadyEi+0x6e [0x824ee3a]
> [1] _ZN9Sequencer17runComputeObjectsEii+0xcc [0x82bbd5c]
> [2] _ZN9Sequencer9integrateEv+0xb04 [0x82c0894]
> [3] _ZN9Sequencer9algorithmEv+0x334 [0x82bb660]
> [4] _ZN9Sequencer9threadRunEPS_+0xc [0x82ccd1c]
> [5] namd2 [0x831aa19]
> [6] Charm++ Runtime: Converse thread (qt_args+0x72 [0x83939ca])
> ~
> Can somebody help me?, please.
> Best wishes
> Jose Correa-Basurto
>
>

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