Re: margin error message

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Jan 24 2006 - 11:11:12 CST

I don't know the role of margin, but try to fix it at 5. I was also facing
same problem which later was solved by fixed margin of 5.

On 1/21/06, surendra negi <negi009_at_yahoo.com> wrote:
>
> Hi all
> during my NPT simulation, I am getting followng error
> message
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP
> 1057000
> WRITING COORDINATES TO DCD FILE AT STEP 1057000
> WRITING COORDINATES TO RESTART FILE AT STEP 1057000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 1057000
> FINISHED WRITING RESTART VELOCITIES
> PRESSURE: 1058000 -16962.5 -30.0279 -2.54154 -30.0279
> -16763.3 -37.908 -2.54154 -37.908 -17312.2
> GPRESSURE: 1058000 224.381 107.672 54.8544 86.4416
> 388.123 138.304 -65.9177 -45.1632 79.508
> PRESSAVG: 1058000 11.4924 14.5574 16.0296 14.5574
> -20.4172 18.8992 16.0296 18.8992 18.6947
> GPRESSAVG: 1058000 12.1517 14.505 15.5661 14.2355
> -20.2581 18.5652 15.4704 18.4933 18.7211
> TIMING: 1058000 CPU: 51836.2, 0.10411/step Wall:
> 62454.7, 0.12298/step, 51.1391 hours remaining, 61363
> kB of memory in use.
> ENERGY: 1058000 1546.5106 4436.9074
> 2466.1088 264.4574 -206359.2041
> 15415.6654 0.0000 0.0000
> 37995.9124 -144233.
> 6421 308.3664 -143915.3105 -143904.6431
> 310.5352 -17012.6840 230.6704
> 636516.6028 3.2566 3.5382
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP
> 1058000
> WRITING COORDINATES TO DCD FILE AT STEP 1058000
> WRITING COORDINATES TO RESTART FILE AT STEP 1058000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 1058000
> 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 am already using margin of 4. Do I need to increase
> it again. I don't know yet. Is there any disadvantage
> of increasing margin beyond 4? if yes please let me
> know.
> thanks in advance
>
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