From: jose correa (corrjose_at_gmail.com)
Date: Fri Jan 23 2009 - 14:27:59 CST
Dear Erica
I am not using the periodic conditions, I have increased the cutoff, but,
the errors still, so, i will reduced the steps and hope works.
Thank you
Jose
2009/1/23 <eprates_at_iqm.unicamp.br>
> Are you simulating using periodic conditions?
> If so, check if the size of the box is not too small... during the
> minimization calculations, the system needs enough space to place the
> atoms in an energetically better configuration. Just an idea...
> Also, I would say that it is better to don't minimize the protein in such
> big number of steps, if you do not want to loose all the structural
> correlation with the crystallyzed structure.
> Bests,
> Érica
>
>
> > Dear all
> > I try to minimized a protein for 10000 steps, but, it does not work, does
> > somebody explain me what happen?. Thank you
> > Info: CREATING 688 COMPUTE OBJECTS
> > Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> > Info: NONBONDED TABLE SIZE: 769 POINTS
> > Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.44089e-16 AT 0.121031
> > Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.04308e-13 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.69407e-21 AT 11.9974
> > Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.09878e-16 AT 11.9974
> > Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295
> > Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974
> > Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138
> > Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974
> > Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
> > 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: Interactive MD listening on port 3000.
> > Info: Entering startup phase 8 with 10528 kB of memory in use.
> > Info: Finished startup with 16424 kB of memory in use.
> > TCL: Minimizing for 10000 steps
> > Warning: Bad global exclusion count, possible error!
> > Warning: Increasing cutoff during minimization may avoid this.
> > PRESSURE: 0 0 0 0 0 0 0 0 0 0
> > GPRESSURE: 0 0 0 0 0 0 0 0 0 0
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP ELECT VDW BOUNDARY
> > MISC KINETIC TOTAL TEMP
> > TOTAL2 TOTAL3 TEMPAVG
> > ENERGY: 0 6615236.8684 99999999.9999 99999999.9999
> > 99999999.9999 -11393.6579 99999999.9999 0.0000
> > 0.0000 0.0000 99999999.9999 0.0000 99999999.9999
> > 99999999.9999 0.0000
> > INITIAL STEP: 1e-06
> > GRADIENT TOLERANCE: nan
> > BRACKET: 0 nan nan nan nan
> > RESTARTING CONJUGATE GRADIENT ALGORITHM
> > INITIAL STEP: 5e-07
> > GRADIENT TOLERANCE: nan
> >
> > Jose Correa-Basurto
> > ESM-IPN, Mexico
> >
>
>
>
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