Custom Search
-- Yong Duan, Ph.D, Professor UC Davis Genome Center and Department of Biomedical Engineering University of California at Davis Davis, CA 95616 530-754-7632 On 12/6/11 9:50 AM, "kirtana S" <skirtana4.gmail.com> 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 > > > 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 >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Dec 06 2011 - 11:30:02 PST