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-- 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 11:27 AM, "kirtana S" <skirtana4.gmail.com> wrote: >I did enenrgy minimization again because my previous run on constant >volume >for 100ps were all using ntc=1 ntf=1 and yesterday your message asked me >to >change this with use of shake (ntc=2, ntf=2) >due to the presence of TIP3P water models.I was mistaken in understand thi >was only for the next steps of MD I interpreted this was for the constnat >volume equilibration > >I am thankful for your suggestions and want to follow them , I changed >thread to avoid complications in following this up . >I did energy minimization now again without using shake (realising the >linmin failures) and then submitted for warming the system (for 70000 >steps >with time step of 0.5 fs) to 50K. > >While heating the ssytem experience sudden rise . Previous runs with >noshake was running alright whereas gave me problems when I tried with >ntc=2 ntf=2 so I change all initial files > >The input file > > 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=2, > 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 output is as below > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.12 PRESS = >0.0 > Etot = -131735.4984 EKtot = 6.8292 EPtot = >-131742.3276 > BOND = 45.8203 ANGLE = 1336.2952 DIHED = >398.4060 > 1-4 NB = 288.7849 1-4 EEL = 7155.9672 VDWAALS = >22723.1972 > EELEC = -163690.7984 EHBOND = 0.0000 RESTRAINT = >0.0000 > Ewald error estimate: 0.1507E-05 > >-------------------------------------------------------------------------- >---- > > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 >========================================================================== >===== > > NSTEP = 500 TIME(PS) = 0.250 TEMP(K) = 113.22 PRESS = >0.0 > Etot = -88875.0006 EKtot = 6625.2647 EPtot = >-95500.2653 > BOND = 60.0946 ANGLE = 1380.3103 DIHED = >437.6682 > 1-4 NB = 293.3695 1-4 EEL = 7165.5473 VDWAALS = >16386.6812 > EELEC = -121314.9083 EHBOND = 0.0000 RESTRAINT = >90.9720 > EAMBER (non-restraint) = -95591.2373 > Ewald error estimate: 0.5773E-04 > >-------------------------------------------------------------------------- >---- > > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 >========================================================================== >===== > > NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 237.67 PRESS = >0.0 > Etot = -73943.6039 EKtot = 13908.2480 EPtot = >-87851.8519 > BOND = 114.9807 ANGLE = 1574.0233 DIHED = >610.6214 > 1-4 NB = 311.8003 1-4 EEL = 7180.5394 VDWAALS = >14639.1175 > EELEC = -113170.4726 EHBOND = 0.0000 RESTRAINT = >887.5381 > EAMBER (non-restraint) = -88739.3900 > Ewald error estimate: 0.1201E-04 > >-------------------------------------------------------------------------- >---- > > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 >========================================================================== >===== > > >I tried changing tautp=0.2 and also removed restraits with nscm=20 , still >there are issues . Can you suggest something on this. > >Thanks >Kirtana > > > > > > >On Tue, Dec 6, 2011 at 2:04 PM, Yong Duan <duan.ucdavis.edu> wrote: > >> >> The ntc=2 was for MD only, not for energy minimization. There is really >>no >> need for energy minimization after you start MD for 100 ps. If you >>indeed >> need to perform energy minimization, we can deal with it later. >> >> Please let me know if you do not want to follow my suggestions. I'd be >> happy to stop. Just in case you still want to try to follow my >> suggestions, please do exactly what I said, continue the MD for 100 ps >> with the exactly the input I told you earlier. It is hard to find out >>what >> went wrong when you change the input parameters. >> >> >> -- >> 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/amber >> >_______________________________________________ >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 - 12:00:04 PST