Re: problems-protein minimization

From: Eduardo Tejera (edutp00_at_yahoo.com)
Date: Mon Jan 26 2009 - 04:04:43 CST

Dear Correa I had the same problem and it was associated with 2 things: an error in the structure (the terminal residues) and a wrong dimension of Periodic Boundary Conditions. Maybe yo wish to inspect the terminals residues.   Best Eduardo ________________________________ De: jose correa <corrjose_at_gmail.com> Para: eprates_at_iqm.unicamp.br; namd-l_at_ks.uiuc.edu Enviado: viernes, 23 de enero, 2009 20:27:59 Asunto: Re: namd-l: problems-protein minimization 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 > ¡Todo sobre la Liga Mexicana de fútbol! Estadisticas, resultados, calendario, fotos y más:&lt; http://espanol.sports.yahoo.com/

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