> Dear All,
>
> When I heat up the simulation box using the following input file after
> minimization using (ntc=2 ntf=2 as recommended for TIP3P water models),
> below are the input files and output files any suggestions are highly
> appreciated.
> minimization of water or solvent molecules
> &cntrl
> imin=1,
> ntb=1,
> cut=10.0,ntc=2,ntf=2,
> maxcyc=10000, ncyc=1000,
> ntt=0,
> &end
>
Your protein may be not getting not minimize. So first you minimize solvent and
ions using restrain on protein then minimized whole system with removing
restrain and dont use shake during minimization.
> heat/dynamics at constant volume
> &cntrl
> imin=0,
> ntxo=1, ntrx=1,
> cut=10.0,tempi=0.1,
> ntpr=500, ntwx=500, ntwe=500,
> nstlim=70000, temp0=50.0,
> dt=0.0005,
> ntc=2, ntf=2, tol=0.0000001,
> ntx=1, irest=0,
> ntb=1,tautp=1,
> ntt=1,
> nmropt=1,ntr=1
> /
> &wt
> type='TEMP0', istep1=0,istep2=70000,value1=0.0, value2=50.0,
> /
> &wt type='END',
> /
> GROUP FOR CONSTRAINTS
> 1.0
> RES 1 336
> END
> END
>
>
> The end of output file of minimization run as below
>
> (restarts due to linmin failure), when I visualize there are no distortions
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2600 -6.7523E+04 8.3420E+00 3.2510E+01 O 13912
>
> BOND = 152.6560 ANGLE = 1964.1433 DIHED =
> 1373.5294
> VDWAALS = 5460.4290 EEL = -83974.9686 HBOND =
> 0.0000
> 1-4 VDW = 446.5435 1-4 EEL = 7054.7245 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2650 -6.7523E+04 8.3420E+00 3.2510E+01 O 13912
>
> BOND = 152.6559 ANGLE = 1964.1432 DIHED =
> 1373.5293
> VDWAALS = 5460.4299 EEL = -83974.9676 HBOND =
> 0.0000
> 1-4 VDW = 446.5434 1-4 EEL = 7054.7247 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2700 -6.7523E+04 8.3420E+00 3.2510E+01 O 13912
>
> BOND = 152.6548 ANGLE = 1964.1401 DIHED =
> 1373.5274
> VDWAALS = 5460.4165 EEL = -83974.9495 HBOND =
> 0.0000
> 1-4 VDW = 446.5427 1-4 EEL = 7054.7239 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2750 -6.7523E+04 8.3420E+00 3.2510E+01 O 13912
>
> BOND = 152.6537 ANGLE = 1964.1379 DIHED =
> 1373.5260
> VDWAALS = 5460.4066 EEL = -83974.9334 HBOND =
> 0.0000
> 1-4 VDW = 446.5420 1-4 EEL = 7054.7236 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2800 -6.7523E+04 8.3420E+00 3.2510E+01 O 13912
>
> BOND = 152.6525 ANGLE = 1964.1346 DIHED =
> 1373.5240
> VDWAALS = 5460.3908 EEL = -83974.9113 HBOND =
> 0.0000
> 1-4 VDW = 446.5412 1-4 EEL = 7054.7228 RESTRAINT =
> 0.0000
>
> ... RESTARTED DUE TO LINMIN FAILURE ...
>
> ***** REPEATED LINMIN FAILURE *****
>
> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2849 -6.7523E+04 8.3420E+00 3.2510E+01 O 13912
>
> BOND = 152.6526 ANGLE = 1964.1344 DIHED =
> 1373.5239
> VDWAALS = 5460.3923 EEL = -83974.9102 HBOND =
> 0.0000
> 1-4 VDW = 446.5411 1-4 EEL = 7054.7227 RESTRAINT =
> 0.0000
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
> --------------------------------------------------------------------------------
>
>
> When I heat the system there is sudden temperature rise and there is job
> failure
>
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 58896.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 58896. NUM_NOSHAKE = 0 CORRECTED RNDFP = 58896.
> | TOTAL # of degrees of freedom (RNDF) = 58896.
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 542540
> | TOTAL SIZE OF NONBOND LIST = 3363880
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.12 PRESS =
> 0.0
> Etot = -67516.1138 EKtot = 6.8292 EPtot =
> -67522.9430
> BOND = 152.6526 ANGLE = 1964.1344 DIHED =
> 1373.5239
> 1-4 NB = 446.5411 1-4 EEL = 7054.7227 VDWAALS =
> 5460.3924
> EELEC = -83974.9102 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.1430E-04
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
> NSTEP = 500 TIME(PS) = 0.250 TEMP(K) = 390.88 PRESS =
> 0.0
> Etot = -43652.3272 EKtot = 22873.9328 EPtot =
> -66526.2600
> BOND = 121.3939 ANGLE = 1830.2706 DIHED =
> 358.2286
> 1-4 NB = 317.7664 1-4 EEL = 7130.6186 VDWAALS =
> 12348.3728
> EELEC = -90162.0935 EHBOND = 0.0000 RESTRAINT =
> 1529.1826
> EAMBER (non-restraint) = -68055.4426
> Ewald error estimate: 0.3642E-03
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
>
> Thanks
> Kirtana
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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Received on Wed Dec 07 2011 - 00:30:03 PST
