From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Sep 07 2017 - 12:15:51 CDT
Hi Natasha,
See http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
Normally, I see this if I did something dumb in system preparation, like
putting atoms on top of one another.
-Josh
On 09/07/2017 10:29 AM, Natasha Gupta wrote:
> Hi,
> I am seeing the following error when trying to minimize my system. Has
> anyone seen this before or do you have suggestions for how to
> troubleshoot?
>
> TCL: Minimizing for 5000 steps
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 83.0912 23.6444 67.9336
> 0.0022 -7726.4852 -nan 0.0000
> 0.0000 0.0000 -nan 0.0000
> -nan -nan 0.0000 -nan
> -nan 31416.0000 -nan -nan
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> MINIMIZER SLOWLY MOVING 6 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY: 1 83.0912 23.6444 67.9336
> 0.0022 -7730.7742 -nan 0.0000
> 0.0000 0.0000 -nan 0.0000
> -nan -nan 0.0000 -nan
> -nan 31416.0000 -nan -nan
>
> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
> FATAL ERROR: Singular matrix in routine ludcmp
>
> Regards,
> Natasha
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