Dear Amber user,
I am running a QM/MM simulation experiment for protein-fructose complex.
During the equilibration phase the density fluctuates and is not converge.
Please, I do not know the reason and how can fix. Please I attached a
sample of the QM/MM data
NSTEP = 1250 TIME(PS) = 57.500 TEMP(K) = 300.60 PRESS =
118.6
Etot = -233282.0322 EKtot = 53567.8624 EPtot =
-286849.8946
BOND = 595.0101 ANGLE = 1380.2578 DIHED =
1817.0370
1-4 NB = 636.7547 1-4 EEL = 3576.4444 VDWAALS =
39121.2262
EELEC = -326902.2505 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7074.3745
EKCMT = 25755.8103 VIRIAL = 23442.4494 VOLUME =
903281.5195
Density =
0.9891
Ewald error estimate: 0.8899E-02
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 58.000 TEMP(K) = 300.86 PRESS =
-55.0
Etot = -233531.4905 EKtot = 53614.7168 EPtot =
-287146.2073
BOND = 558.4646 ANGLE = 1377.7387 DIHED =
1819.0675
1-4 NB = 643.6186 1-4 EEL = 3653.3120 VDWAALS =
38902.8888
EELEC = -327007.5922 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7093.7053
EKCMT = 25856.0850 VIRIAL = 26928.9378 VOLUME =
902885.2100
Density =
0.9895
Ewald error estimate: 0.8859E-02
------------------------------------------------------------------------------
NSTEP = 1750 TIME(PS) = 58.500 TEMP(K) = 298.77 PRESS =
9.7
Etot = -233908.7061 EKtot = 53241.8729 EPtot =
-287150.5791
BOND = 586.4987 ANGLE = 1468.8395 DIHED =
1813.3994
1-4 NB = 637.0498 1-4 EEL = 3577.6409 VDWAALS =
38878.6836
EELEC = -327049.8878 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7062.8031
EKCMT = 25682.8725 VIRIAL = 25493.3004 VOLUME =
902599.4024
Density =
0.9898
Ewald error estimate: 0.8806E-02
------------------------------------------------------------------------------
NSTEP = 2000 TIME(PS) = 59.000 TEMP(K) = 302.35 PRESS =
-11.2
Etot = -233452.9431 EKtot = 53881.0902 EPtot =
-287334.0333
BOND = 613.8656 ANGLE = 1464.8649 DIHED =
1799.1951
1-4 NB = 638.7601 1-4 EEL = 3587.4948 VDWAALS =
38694.9632
EELEC = -327047.9936 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7085.1835
EKCMT = 25851.8674 VIRIAL = 26069.6569 VOLUME =
902542.1383
Density =
0.9899
NSTEP = 3500 TIME(PS) = 63.000 TEMP(K) = 299.42 PRESS =
-50.6
Etot = -233553.0579 EKtot = 53358.6820 EPtot =
-286911.7399
BOND = 550.2453 ANGLE = 1423.5704 DIHED =
1802.9575
1-4 NB = 641.5385 1-4 EEL = 3610.8307 VDWAALS =
38792.3917
EELEC = -326351.2844 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7381.9897
EKCMT = 25584.4201 VIRIAL = 26579.1899 VOLUME =
910426.3527
Density =
0.9813
Ewald error estimate: 0.2647E-01
------------------------------------------------------------------------------
NSTEP = 3750 TIME(PS) = 63.500 TEMP(K) = 300.15 PRESS =
108.9
Etot = -233367.0651 EKtot = 53488.6369 EPtot =
-286855.7020
BOND = 566.9434 ANGLE = 1448.7261 DIHED =
1800.2155
1-4 NB = 640.1630 1-4 EEL = 3587.0528 VDWAALS =
39133.7274
EELEC = -326551.8002 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7480.7301
EKCMT = 25746.0899 VIRIAL = 23606.5655 VOLUME =
909976.7292
Density =
0.9818
Ewald error estimate: 0.2634E-01
------------------------------------------------------------------------------
NSTEP = 4000 TIME(PS) = 64.000 TEMP(K) = 301.62 PRESS =
79.2
Etot = -233097.4345 EKtot = 53750.9879 EPtot =
-286848.4224
BOND = 604.3186 ANGLE = 1411.7011 DIHED =
1811.7121
1-4 NB = 635.4322 1-4 EEL = 3610.5240 VDWAALS =
39132.1436
EELEC = -326547.0891 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7507.1649
EKCMT = 25817.1578 VIRIAL = 24259.5613 VOLUME =
910729.0269
Density =
0.9810
Ewald error estimate: 0.2655E-01
------------------------------------------------------------------------------
NSTEP = 4250 TIME(PS) = 64.500 TEMP(K) = 300.04 PRESS =
-86.7
Etot = -233314.0522 EKtot = 53469.4988 EPtot =
-286783.5510
BOND = 577.6774 ANGLE = 1432.0203 DIHED =
1798.3627
1-4 NB = 627.4001 1-4 EEL = 3636.2253 VDWAALS =
38477.4250
EELEC = -325844.3464 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7488.3154
EKCMT = 25593.9489 VIRIAL = 27298.5533 VOLUME =
910662.4106
Density =
0.9811
Ewald error estimate: 0.2662E-01
------------------------------------------------------------------------------
NSTEP = 4500 TIME(PS) = 65.000 TEMP(K) = 301.33 PRESS =
11.3
Etot = -233055.9826 EKtot = 53698.4202 EPtot =
-286754.4029
BOND = 573.6731 ANGLE = 1441.5820 DIHED =
1791.1233
1-4 NB = 644.3046 1-4 EEL = 3626.6938 VDWAALS =
38996.2492
EELEC = -326317.1325 EHBOND = 0.0000 RESTRAINT =
0.0000
DFTBESCF= -7510.8962
EKCMT = 25864.9992 VIRIAL = 25642.4522 VOLUME =
910509.7489
Density =
0.9812
Ewald error estimate: 0.2634E-01
Any suggestion will be appreciated,
Ibrahim
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Received on Fri Jun 21 2013 - 13:30:02 PDT
