dear Amber users,
I encountered a problem while running Targeted MD in Amber9. It was a 5ns
simulation, and recorded a snapshot for every 10ps, which means that 500
snapshots should have been produced. But when I extracted PDB from the mdcrd
file, *the last 40 snapshots were 0 byte*. The first 460 snapshots were OK,
but in this sense, I can't get the final structure that I want.
I've tried this for three times, but the results were the same.
The input and output files are as follows. Please tell me if anything was
wrong? What should I do? Thanks a lot!
Here is the input file:
&cntrl
imin = 0, ntx = 1, nstlim = 2500000,
irest=0,
dt = 0.002, ntc = 2, ntf = 2, tol =
0.000001,
tempi = 100.0, temp0 =
300.0,
scee = 1.2, cut =
10.0,
ntpr = 500, ntwx = 5000, ntwr =
5000,
ntb = 2, ntt = 1, tautp = 0.5, ntp =
0,
nscm = 0, nmropt =
1,
ntr = 1, pres0 = 1.0, ntp =
1,
restraintmask=":1-231.CA", restraint_wt =
1
itgtmd = 1, tgtrmsd = 22.3, tgtmdfrc =
0.1,
tgtrmsmask=":232-267.CA",
/
&wt
TYPE='TGTRMSD', istep1=1,
istep2=2500000,
value1 = 21, value2 =
0.0,
/
&wt
type="END",
/
Here is the output from 4595ps to 4603ps. *I don't see any difference
between the results before and after 4600ps.
But it seems that the "current RMSD from reference" failed to continue to
decline after 4600 ps.
*
===============================================================================
NSTEP = 2297500 TIME(PS) = 4595.000 TEMP(K) = 300.21 PRESS =
-107.7
Etot = -112922.8799 EKtot = 27874.5311 EPtot =
-140797.4110
BOND = 762.9742 ANGLE = 2049.4000 DIHED =
2614.1876
1-4 NB = 979.3344 1-4 EEL = 9477.3217 VDWAALS =
17075.5534
EELEC = -173856.7656 EHBOND = 0.0000 RESTRAINT =
100.5833
EAMBER (non-restraint) = -140897.9943
EKCMT = 12449.6916 VIRIAL = 13516.2395 VOLUME =
458830.0372
Density =
1.0079
Ewald error estimate: 0.7310E-04
Current RMSD from reference: 6.636
Current target RMSD: 1.701
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2298000 TIME(PS) = 4596.000 TEMP(K) = 300.07 PRESS =
-48.1
Etot = -112951.5815 EKtot = 27861.0188 EPtot =
-140812.6004
BOND = 811.1621 ANGLE = 2013.6258 DIHED =
2625.8966
1-4 NB = 1005.8037 1-4 EEL = 9505.7996 VDWAALS =
16830.0358
EELEC = -173700.5998 EHBOND = 0.0000 RESTRAINT =
95.6756
EAMBER (non-restraint) = -140908.2760
EKCMT = 12565.2794 VIRIAL = 13042.5954 VOLUME =
459219.3934
Density =
1.0071
Ewald error estimate: 0.3627E-04
Current RMSD from reference: 6.625
Current target RMSD: 1.697
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2298500 TIME(PS) = 4597.000 TEMP(K) = 298.80 PRESS =
304.7
Etot = -112931.2817 EKtot = 27743.5229 EPtot =
-140674.8046
BOND = 743.7103 ANGLE = 2043.0138 DIHED =
2622.1245
1-4 NB = 1005.1307 1-4 EEL = 9554.9015 VDWAALS =
17054.5584
EELEC = -173793.8218 EHBOND = 0.0000 RESTRAINT =
95.5779
EAMBER (non-restraint) = -140770.3825
EKCMT = 12338.2988 VIRIAL = 9323.1586 VOLUME =
458345.6915
Density =
1.0090
Ewald error estimate: 0.7251E-04
Current RMSD from reference: 6.566
Current target RMSD: 1.693
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2299000 TIME(PS) = 4598.000 TEMP(K) = 299.59 PRESS =
87.9
Etot = -112925.2656 EKtot = 27816.7212 EPtot =
-140741.9867
BOND = 767.9026 ANGLE = 1971.8877 DIHED =
2617.6127
1-4 NB = 1006.1232 1-4 EEL = 9576.9773 VDWAALS =
16987.7026
EELEC = -173779.1189 EHBOND = 0.0000 RESTRAINT =
108.9261
EAMBER (non-restraint) = -140850.9129
EKCMT = 12369.4621 VIRIAL = 11499.4378 VOLUME =
458595.4466
Density =
1.0085
Ewald error estimate: 0.1430E-03
Current RMSD from reference: 6.568
Current target RMSD: 1.688
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2299500 TIME(PS) = 4599.000 TEMP(K) = 301.28 PRESS =
-136.4
Etot = -112922.7510 EKtot = 27973.6420 EPtot =
-140896.3930
BOND = 779.0589 ANGLE = 2013.8339 DIHED =
2630.8286
1-4 NB = 966.1179 1-4 EEL = 9565.8508 VDWAALS =
16874.2219
EELEC = -173830.5438 EHBOND = 0.0000 RESTRAINT =
104.2389
EAMBER (non-restraint) = -141000.6320
EKCMT = 12491.4867 VIRIAL = 13842.6634 VOLUME =
458803.1823
Density =
1.0080
Ewald error estimate: 0.1014E-03
Current RMSD from reference: 6.610
Current target RMSD: 1.684
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2300000 TIME(PS) = 4600.000 TEMP(K) = 297.31 PRESS =
-74.1
Etot = -112986.9622 EKtot = 27605.0408 EPtot =
-140592.0031
BOND = 793.3833 ANGLE = 2079.8847 DIHED =
2609.6260
1-4 NB = 982.0757 1-4 EEL = 9521.0395 VDWAALS =
16808.6632
EELEC = -173497.4425 EHBOND = 0.0000 RESTRAINT =
110.7671
EAMBER (non-restraint) = -140702.7702
EKCMT = 12439.3454 VIRIAL = 13172.1104 VOLUME =
458303.6580
Density =
1.0091
Ewald error estimate: 0.3151E-04
Current RMSD from reference: 6.697
Current target RMSD: 1.680
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2300500 TIME(PS) = 4601.000 TEMP(K) = 300.26 PRESS =
36.9
Etot = -112941.9275 EKtot = 27879.1802 EPtot =
-140821.1077
BOND = 793.8926 ANGLE = 2029.8834 DIHED =
2617.5255
1-4 NB = 975.2133 1-4 EEL = 9527.6610 VDWAALS =
16992.6146
EELEC = -173856.1217 EHBOND = 0.0000 RESTRAINT =
98.2235
EAMBER (non-restraint) = -140919.3313
EKCMT = 12441.6280 VIRIAL = 12075.9965 VOLUME =
458380.6248
Density =
1.0089
Ewald error estimate: 0.8431E-04
Current RMSD from reference: 6.761
Current target RMSD: 1.676
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2301000 TIME(PS) = 4602.000 TEMP(K) = 300.36 PRESS =
-122.3
Etot = -112971.3676 EKtot = 27888.7501 EPtot =
-140860.1177
BOND = 786.3316 ANGLE = 1964.7559 DIHED =
2600.6188
1-4 NB = 967.4038 1-4 EEL = 9598.9393 VDWAALS =
16698.9511
EELEC = -173578.4232 EHBOND = 0.0000 RESTRAINT =
101.3049
EAMBER (non-restraint) = -140961.4226
EKCMT = 12528.7212 VIRIAL = 13740.2368 VOLUME =
458909.8050
Density =
1.0078
Ewald error estimate: 0.7599E-04
Current RMSD from reference: 6.666
Current target RMSD: 1.672
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2301500 TIME(PS) = 4603.000 TEMP(K) = 300.53 PRESS =
-9.4
Etot = -112920.7674 EKtot = 27903.9403 EPtot =
-140824.7078
BOND = 784.2054 ANGLE = 2033.5866 DIHED =
2603.3653
1-4 NB = 1010.5177 1-4 EEL = 9579.4754 VDWAALS =
16958.9542
EELEC = -173893.3966 EHBOND = 0.0000 RESTRAINT =
98.5842
EAMBER (non-restraint) = -140923.2919
EKCMT = 12465.6655 VIRIAL = 12558.9569 VOLUME =
458930.7429
Density =
1.0077
Ewald error estimate: 0.1082E-03
Current RMSD from reference: 6.725
Current target RMSD: 1.667
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Received on Tue Nov 30 2010 - 01:30:03 PST
