Thanks for explaining this I will work on this accordingly.
Kirtana
On Tue, Dec 6, 2011 at 2:56 PM, Yong Duan <duan.ucdavis.edu> wrote:
>
> Your previous runs without shake were ok because you used 0.5fs time step
> and at 50K. For production runs, the typical time step is 1-2fs and
> temperature is typically at 300K. When you change to dt=1fs, temp0=300K,
> the system would crash almost immediately with NTC=1.
>
> Now, I lost track of what you've done and can no longer make any further
> suggestions.
>
>
> --
> 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
> >> >_______________________________________________
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> >> >AMBER.ambermd.org
> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
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Received on Tue Dec 06 2011 - 12:30:03 PST
