From: Stern, Julie (jvstern_at_bnl.gov)
Date: Thu Apr 14 2005 - 16:53:15 CDT
I did check that and fixed the problem. I had different dimensions in the
.incprd file than I did in the config file, but I made them the same. And
the problem still occurred.
-----Original Message-----
From: Pijush Ghosh
To: Stern, Julie
Sent: 4/14/2005 5:48 PM
Subject: Re: namd-l: minimization problem
Julie
i dont know if you have got my earlier message, but yes seeing your
error message i have a kind of feelings that your system is turning
unstable and one reason could be inaccurate cell dimension.
----- Original Message -----
From: "Stern, Julie" <jvstern_at_bnl.gov>
To: <namd-l_at_ks.uiuc.edu>
Sent: Thursday, April 14, 2005 3:26 PM
Subject: RE: namd-l: minimization problem
> Here are the energies:
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP
> ELECT VDW BOUNDARY MISC
KINETIC
> TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
>
> ENERGY: 0 472.7316 49.3810 -99999999.9999
> 0.0000
> 16167.5620 99999999.9999 0.0000 0.0000
0.0000
> -99999999.9999 0.0000 -99999999.9999 -99999999.9999
0.0000
> -99999999.9999 -99999999.9999 61866.4212 -99999999.9999
-99999999.9999
>
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
>
>
>
> -----Original Message-----
> From: Brian Bennion
> To: Stern, Julie
> Sent: 4/14/2005 4:12 PM
> Subject: Re: namd-l: minimization problem
>
>
> Can you give us some more information? Like say, what are the
energies
> before this step is printed in the log file?
>
>
>
> On Thu, 14 Apr 2005, Stern, Julie wrote:
>
>> What does it mean if during minimization is says:
>> INITIAL STEP: 1e-06
>> GRADIENT TOLERANCE: nan
>>
>> and then just sits there. How do I fix this?
>>
>> Thanks.
>>
>> --Julie
>>
>
> ************************************************
> Brian Bennion, Ph.D.
> Bioscience Directorate
> Lawrence Livermore National Laboratory
> P.O. Box 808, L-448 bennion1_at_llnl.gov
> 7000 East Avenue phone: (925) 422-5722
> Livermore, CA 94550 fax: (925) 424-6605
> ************************************************
>
>
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