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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Received on Tue Dec 06 2011 - 10:00:02 PST
