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
Received on Tue Dec 06 2011 - 11:30:03 PST
