hello amber users,
I am using the sander for md simulation during the process it was
terminating in the middle and the out in the heat.out file was like this
*sander -O -i heat.in -o heat.out -p pdb1k4u_apo2_sol.prmtop -c min.rst -r
heat.rst -x heat.mdcrd -ref min.rst*
*Output:-*
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 03/24/2011 at 10:21:13
[-O]verwriting output
File Assignments:
| MDIN: heat.in
| MDOUT: heat.out
|INPCRD: min.rst
| PARM: pdb1k4u_apo2_sol.prmtop
|RESTRT: heat.rst
| REFC: min.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: heat.mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
heat pdb1k4u_apo2
&cntrl
imin=0,irest=0,ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
ntr=1,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
BlAH
2.0
RES 1 242
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 32.368
| New format PARM file being parsed.
| Version = 1.000 Date = 03/23/11 Time = 00:31:52
NATOM = 24182 NTYPES = 16 NBONH = 23441 MBONA = 753
NTHETH = 1721 MTHETA = 1017 NPHIH = 3206 MPHIA = 2555
NHPARM = 0 NPARM = 0 NNB = 38524 NRES = 7659
NBONA = 753 NTHETA = 1017 NPHIA = 2555 NUMBND = 47
NUMANG = 87 NPTRA = 41 NATYP = 35 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1342688
| Hollerith 80207
| Integer 828340
| Max Pairs 8060666
| nblistReal 290184
| nblist Int 1300633
| Total 52873 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 25000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 64.737 Box Y = 70.948 Box Z = 67.136
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 64 NFFT2 = 72 NFFT3 = 72
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
BlAH
GROUP 1 HAS HARMONIC CONSTRAINTS 2.00000
GRP 1 RES 1 TO 242
Number of atoms in this group = 1931
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 25000 0.100000 300.000000 0 0
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 7564
Sum of charges from parm topology file = -3.00000003
Assuming uniform neutralizing plasma
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 49105.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 49105. NUM_NOSHAKE = 0 CORRECTED RNDFP = 49105.
| TOTAL # of degrees of freedom (RNDF) = 49105.
---------------------------------------------------
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 = 4134189
| TOTAL SIZE OF NONBOND LIST = 4134189
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -67866.2635 EKtot = 0.0000 EPtot =
-67866.2635
BOND = 31.0171 ANGLE = 169.8340 DIHED =
1090.8243
1-4 NB = 424.8482 1-4 EEL = 4660.1412 VDWAALS =
4589.3108
EELEC = -78832.2390 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.7614E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 47.66 PRESS =
0.0
Etot = -85453.1115 EKtot = 2325.4435 EPtot =
-87778.5550
BOND = 43.4984 ANGLE = 206.9241 DIHED =
1002.0524
1-4 NB = 342.7681 1-4 EEL = 4572.8643 VDWAALS =
15581.9365
EELEC = -109890.0083 EHBOND = 0.0000 RESTRAINT =
361.4094
EAMBER (non-restraint) = -88139.9645
Ewald error estimate: 0.2329E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 18.63 PRESS =
0.0
Etot = -89269.2449 EKtot = 908.9589 EPtot =
-90178.2037
BOND = 41.6598 ANGLE = 205.1703 DIHED =
1003.6214
1-4 NB = 345.2256 1-4 EEL = 4582.3395 VDWAALS =
17090.0126
EELEC = -113778.0157 EHBOND = 0.0000 RESTRAINT =
331.7828
EAMBER (non-restraint) = -90509.9866
Ewald error estimate: 0.3114E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 17.59 PRESS =
0.0
Etot = -89721.9185 EKtot = 858.2083 EPtot =
-90580.1268
BOND = 48.4207 ANGLE = 210.8804 DIHED =
1001.3563
1-4 NB = 347.9077 1-4 EEL = 4577.7689 VDWAALS =
17267.1602
EELEC = -114356.4861 EHBOND = 0.0000 RESTRAINT =
322.8651
EAMBER (non-restraint) = -90902.9919
Ewald error estimate: 0.1980E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 22.00 PRESS =
0.0
Etot = -89430.1844 EKtot = 1073.3741 EPtot =
-90503.5585
BOND = 49.6331 ANGLE = 219.5662 DIHED =
1006.0362
1-4 NB = 347.5233 1-4 EEL = 4572.7148 VDWAALS =
17255.5088
EELEC = -114278.2281 EHBOND = 0.0000 RESTRAINT =
323.6872
EAMBER (non-restraint) = -90827.2457
Ewald error estimate: 0.2090E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2500 TIME(PS) = 5.000 TEMP(K) = 27.74 PRESS =
0.0
Etot = -89008.9434 EKtot = 1353.4825 EPtot =
-90362.4259
BOND = 58.4709 ANGLE = 236.9170 DIHED =
1008.8628
1-4 NB = 348.7314 1-4 EEL = 4569.0384 VDWAALS =
17189.9260
EELEC = -114103.0239 EHBOND = 0.0000 RESTRAINT =
328.6515
EAMBER (non-restraint) = -90691.0774
Ewald error estimate: 0.2593E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 33.60 PRESS =
0.0
Etot = -88503.6628 EKtot = 1639.3219 EPtot =
-90142.9847
BOND = 65.6348 ANGLE = 245.9596 DIHED =
1007.8235
1-4 NB = 349.7460 1-4 EEL = 4572.6333 VDWAALS =
17019.4238
EELEC = -113744.3925 EHBOND = 0.0000 RESTRAINT =
340.1869
EAMBER (non-restraint) = -90483.1716
Ewald error estimate: 0.2305E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 39.08 PRESS =
0.0
Etot = -88019.0265 EKtot = 1906.5905 EPtot =
-89925.6170
BOND = 63.2188 ANGLE = 256.4110 DIHED =
1013.9218
1-4 NB = 348.6459 1-4 EEL = 4587.8149 VDWAALS =
16991.6064
EELEC = -113525.9987 EHBOND = 0.0000 RESTRAINT =
338.7630
EAMBER (non-restraint) = -90264.3800
Ewald error estimate: 0.2235E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 44.89 PRESS =
0.0
Etot = -87487.5513 EKtot = 2190.4102 EPtot =
-89677.9615
BOND = 70.5605 ANGLE = 267.6956 DIHED =
1013.6091
1-4 NB = 352.1245 1-4 EEL = 4581.7202 VDWAALS =
16856.0294
EELEC = -113149.4318 EHBOND = 0.0000 RESTRAINT =
329.7311
EAMBER (non-restraint) = -90007.6926
Ewald error estimate: 0.2511E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 51.23 PRESS =
0.0
Etot = -86949.7560 EKtot = 2499.7782 EPtot =
-89449.5342
BOND = 74.2649 ANGLE = 274.6854 DIHED =
1010.1647
1-4 NB = 348.0945 1-4 EEL = 4577.9661 VDWAALS =
16890.9233
EELEC = -112959.6407 EHBOND = 0.0000 RESTRAINT =
334.0074
EAMBER (non-restraint) = -89783.5417
Ewald error estimate: 0.2989E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 57.09 PRESS =
0.0
Etot = -86383.6060 EKtot = 2785.6540 EPtot =
-89169.2600
BOND = 80.1776 ANGLE = 291.2072 DIHED =
1015.6714
1-4 NB = 353.7537 1-4 EEL = 4582.2307 VDWAALS =
16656.8709
EELEC = -112502.2074 EHBOND = 0.0000 RESTRAINT =
353.0360
EAMBER (non-restraint) = -89522.2960
Ewald error estimate: 0.2921E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 5500 TIME(PS) = 11.000 TEMP(K) = 63.42 PRESS =
0.0
Etot = -85829.5087 EKtot = 3094.1893 EPtot =
-88923.6981
BOND = 77.0232 ANGLE = 309.7384 DIHED =
1012.8366
1-4 NB = 355.3480 1-4 EEL = 4593.4603 VDWAALS =
16624.8220
EELEC = -112237.7220 EHBOND = 0.0000 RESTRAINT =
340.7954
EAMBER (non-restraint) = -89264.4935
Ewald error estimate: 0.3281E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 68.70 PRESS =
0.0
Etot = -85352.8414 EKtot = 3351.7417 EPtot =
-88704.5830
BOND = 85.4318 ANGLE = 318.3891 DIHED =
1020.2065
1-4 NB = 353.6599 1-4 EEL = 4583.8022 VDWAALS =
16618.2103
EELEC = -112037.8932 EHBOND = 0.0000 RESTRAINT =
353.6104
EAMBER (non-restraint) = -89058.1934
Ewald error estimate: 0.3406E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 6500 TIME(PS) = 13.000 TEMP(K) = 75.35 PRESS =
0.0
Etot = -84795.5885 EKtot = 3676.5201 EPtot =
-88472.1086
BOND = 93.3939 ANGLE = 331.9302 DIHED =
1019.2704
1-4 NB = 354.4867 1-4 EEL = 4586.6428 VDWAALS =
16343.5169
EELEC = -111568.0050 EHBOND = 0.0000 RESTRAINT =
366.6556
EAMBER (non-restraint) = -88838.7642
Ewald error estimate: 0.2858E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 81.70 PRESS =
0.0
Etot = -84231.4324 EKtot = 3986.2318 EPtot =
-88217.6642
BOND = 91.0481 ANGLE = 331.4721 DIHED =
1022.4532
1-4 NB = 357.9641 1-4 EEL = 4573.0827 VDWAALS =
16436.7602
EELEC = -111396.0460 EHBOND = 0.0000 RESTRAINT =
365.6016
EAMBER (non-restraint) = -88583.2658
Ewald error estimate: 0.3731E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 7500 TIME(PS) = 15.000 TEMP(K) = 88.20 PRESS =
0.0
Etot = -83664.6370 EKtot = 4303.5114 EPtot =
-87968.1484
BOND = 105.3223 ANGLE = 342.3931 DIHED =
1014.6877
1-4 NB = 354.3987 1-4 EEL = 4585.1425 VDWAALS =
16297.6518
EELEC = -111042.1434 EHBOND = 0.0000 RESTRAINT =
374.3989
EAMBER (non-restraint) = -88342.5473
Ewald error estimate: 0.3299E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 93.03 PRESS =
0.0
Etot = -83169.4618 EKtot = 4538.9027 EPtot =
-87708.3646
BOND = 103.9290 ANGLE = 352.7595 DIHED =
1032.9506
1-4 NB = 361.4146 1-4 EEL = 4582.1795 VDWAALS =
16100.3950
EELEC = -110608.5699 EHBOND = 0.0000 RESTRAINT =
366.5770
EAMBER (non-restraint) = -88074.9416
Ewald error estimate: 0.3722E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 8500 TIME(PS) = 17.000 TEMP(K) = 99.27 PRESS =
0.0
Etot = -82627.3099 EKtot = 4843.2214 EPtot =
-87470.5313
BOND = 113.5459 ANGLE = 362.8084 DIHED =
1027.5293
1-4 NB = 356.3530 1-4 EEL = 4589.4224 VDWAALS =
16074.2522
EELEC = -110361.3148 EHBOND = 0.0000 RESTRAINT =
366.8723
EAMBER (non-restraint) = -87837.4036
Ewald error estimate: 0.3323E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 105.37 PRESS =
0.0
Etot = -82115.5757 EKtot = 5141.0624 EPtot =
-87256.6381
BOND = 119.1134 ANGLE = 374.1381 DIHED =
1036.3070
1-4 NB = 357.5211 1-4 EEL = 4560.3641 VDWAALS =
16001.5727
EELEC = -110093.3922 EHBOND = 0.0000 RESTRAINT =
387.7377
EAMBER (non-restraint) = -87644.3759
Ewald error estimate: 0.3482E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
"heat.out" 424L, 22218C written
Can any check this and tell me where the problem occurs.
Regards,
Vani
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Received on Thu Mar 24 2011 - 11:00:03 PDT
