Re: scripting problem

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Mon Jan 25 2010 - 01:04:06 CST

the output tells you what is going wrong:
the electrostatic and VDW energies indicate that your system is screwed up.
Maybe, you have too close atoms in your system.
You may also want to check the unit cell vectors.

BTW I do not see any temperature definition in your input.

eddie

PS: it is not a good idea t include the input file as a word file! Plain
text is better.

On Mon, Jan 25, 2010 at 12:15 AM, ipsita basu <ibasu788_at_gmail.com> wrote:

> Dear all,
> I want to run simulation of a previously equilibrated bilayer.
> But the problem is that after some time the job is aborted. My input is
> attached with this mail. What should I done to solve this? The error part is
> given below:
> Info: LARGEST PATCH (21) HAS 10791 ATOMS
> Info: CREATING 2469 COMPUTE OBJECTS
> Info: Entering startup phase 4 with 27816 kB of memory in use.
> Info: PME using 1 and 1 processors for FFT and reciprocal sum.
> Info: PME GRID LOCATIONS: 0
> Info: PME TRANS LOCATIONS: 0
> Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
> Info: Entering startup phase 5 with 29048 kB of memory in use.
> Info: Entering startup phase 6 with 29048 kB of memory in use.
> Measuring processor speeds... Done.
> Info: Entering startup phase 7 with 29048 kB of memory in use.
> Info: CREATING 2469 COMPUTE OBJECTS
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.70577e-22 AT 11.9974
> Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 6.62384e-17 AT 11.9974
> Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE:
> 2.91168e-22 AT 11.9974
> Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 4.21309e-16 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 3.17637e-22 AT 11.9974
> Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 6.72001e-17 AT 11.9974
> ....
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138
> Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
> Info: Entering startup phase 8 with 30392 kB of memory in use.
> Info: Finished startup with 33976 kB of memory in use
> TCL: Minimizing for 5000 steps
> PRESSURE: 0 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
> GPRESSAVG
>
> ENERGY: 0 2800530.4389 631684.4468 4744.6505
> 65.6101 99999999.9999 99999999.9999 0.0000 0.0000
> 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999
> 0.0000 nan nan 259701.4139 99999999.9999
> 99999999.9999
> 259701.4139 99999999.9999 99999999.9999
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 2.5e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> ......
> INITIAL STEP: 1e-300
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
>
> So please help me .
>
>
> Thanking You
>
> Ipsita Basu
>
>
>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================================================

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