My simulation run has good enengetics for a high solute concentration about
(by wt%) and also goes through ,whereas when I use this fo a 50wt% of
solute concentration I get severe temperature
rise .
During heating , what should I use to control the temperature (I tried
tautp=1 and tautp=2) , I have ions in my system .
Thanks
Kirtana
On Wed, Dec 7, 2011 at 3:13 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> > 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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> > AMBER.ambermd.org
> > 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
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>
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Received on Wed Dec 07 2011 - 13:00:03 PST
