AMBER Archive (2003)

Subject: AMBER: problems with pmemd

From: james tomomi macdonald (j.macdonald_at_mail.cryst.bbk.ac.uk)
Date: Fri Aug 22 2003 - 10:37:34 CDT

Hi,

I am experiencing another strange error with pmemd, which is probably
connected to my previous problems!

I have been running a constant pressure/temperature at 300K simulation for
almost 5ns, when suddenly the temperature jumped to over 500K, then
gradually fell back. I visually looked at the crd file with VMD, and you
observe at this point that all the atoms move in a concerted motion in one
direction, and you can also see layers of high and low water density
appear.

I then tried running exactly the same simulation with the same restart
file and the same parameters on sander7, and this did not occur. I show
the relevent parts of the output files below:

pmemd:

 NSTEP = 6500 TIME(PS) = 4961.500 TEMP(K) = 298.47 PRESS = 63.3
 Etot = -41733.7676 EKtot = 10194.6513 EPtot = -51928.4189
 BOND = 292.5101 ANGLE = 728.0762 DIHED = 845.7586
 1-4 NB = 310.2881 1-4 EEL = 3978.8609 VDWAALS = 6489.8158
 EELEC = -64573.7287 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4626.5850 VIRIAL = 4395.7938 VOLUME = 168813.4283
                                                Density = 1.0135
 Ewald error estimate: 0.7729E-06
 
------------------------------------------------------------------------------

 NSTEP = 6600 TIME(PS) = 4961.600 TEMP(K) = 318.95 PRESS = 289.9
 Etot = -39330.7480 EKtot = 10894.0969 EPtot = -50224.8450
 BOND = 270.7332 ANGLE = 774.0337 DIHED = 856.7722
 1-4 NB = 308.1194 1-4 EEL = 3962.1139 VDWAALS = 6547.6415
 EELEC = -62944.2589 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4810.6653 VIRIAL = 3754.2828 VOLUME = 168777.5285
                                                Density = 1.0137
 Ewald error estimate: 0.1708E-01
 
------------------------------------------------------------------------------

 NSTEP = 6700 TIME(PS) = 4961.700 TEMP(K) = 357.95 PRESS = 286.2
 Etot = -36504.3138 EKtot = 12226.1990 EPtot = -48730.5128
 BOND = 321.2632 ANGLE = 747.7915 DIHED = 846.2733
 1-4 NB = 315.5974 1-4 EEL = 3960.5898 VDWAALS = 6010.7395
 EELEC = -60932.7674 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 5114.1891 VIRIAL = 4058.7757 VOLUME = 170772.0682
                                                Density = 1.0018
 Ewald error estimate: 0.1601E-01
 
------------------------------------------------------------------------------

 NSTEP = 6800 TIME(PS) = 4961.800 TEMP(K) = 390.12 PRESS = 418.9
 Etot = -34301.1423 EKtot = 13324.8770 EPtot = -47626.0194
 BOND = 298.6391 ANGLE = 820.5181 DIHED = 844.3443
 1-4 NB = 308.4515 1-4 EEL = 3940.1651 VDWAALS = 5379.3324
 EELEC = -59217.4698 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 5403.9209 VIRIAL = 3836.1876 VOLUME = 173353.0579
                                                Density = 0.9869
 Ewald error estimate: 0.7236E-02
 
------------------------------------------------------------------------------

 NSTEP = 6900 TIME(PS) = 4961.900 TEMP(K) = 421.96 PRESS = 785.4
 Etot = -31076.8311 EKtot = 14412.2642 EPtot = -45489.0952
 BOND = 294.2989 ANGLE = 779.3968 DIHED = 879.6072
 1-4 NB = 317.9626 1-4 EEL = 3941.5282 VDWAALS = 5084.2504
 EELEC = -56786.1392 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 5864.7529 VIRIAL = 2877.9554 VOLUME = 176136.6267
                                                Density = 0.9713
 Ewald error estimate: 0.1240E-02
 
------------------------------------------------------------------------------

check COM velocity, temp: 0.008719 0.11(Removed)

 NSTEP = 7000 TIME(PS) = 4962.000 TEMP(K) = 452.71 PRESS = 1121.2
 Etot = -30028.8195 EKtot = 15462.6471 EPtot = -45491.4666
 BOND = 289.4439 ANGLE = 755.1666 DIHED = 866.9537
 1-4 NB = 309.4601 1-4 EEL = 3951.9019 VDWAALS = 4989.5962
 EELEC = -56653.9891 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 6272.9548 VIRIAL = 1928.5536 VOLUME = 179455.1194
                                                Density = 0.9534
 Ewald error estimate: 0.2364E-01
 
------------------------------------------------------------------------------

 NSTEP = 7100 TIME(PS) = 4962.100 TEMP(K) = 474.42 PRESS = 1377.2
 Etot = -26714.0726 EKtot = 16204.0949 EPtot = -42918.1674
 BOND = 295.2772 ANGLE = 766.4333 DIHED = 892.7033
 1-4 NB = 302.5419 1-4 EEL = 3953.6028 VDWAALS = 4702.3717
 EELEC = -53831.0978 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 6460.5940 VIRIAL = 1018.1852 VOLUME = 183029.9082
                                                Density = 0.9347
 Ewald error estimate: 0.3551E-02
 
------------------------------------------------------------------------------

 NSTEP = 7200 TIME(PS) = 4962.200 TEMP(K) = 505.94 PRESS = 1294.1
 Etot = -26808.0582 EKtot = 17280.7629 EPtot = -44088.8211
 BOND = 300.5836 ANGLE = 748.5357 DIHED = 874.6213
 1-4 NB = 315.1921 1-4 EEL = 3922.2050 VDWAALS = 4535.0485
 EELEC = -54785.0072 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 6913.5681 VIRIAL = 1690.8046 VOLUME = 186915.4954
                                                Density = 0.9153
 Ewald error estimate: 0.8253E-01
 
------------------------------------------------------------------------------

sander 7:

 NSTEP = 6500 TIME(PS) = 4961.500 TEMP(K) = 301.21 PRESS = -62.9
 Etot = -41834.7763 EKtot = 10287.9979 EPtot = -52122.7742
 BOND = 274.5862 ANGLE = 728.2804 DIHED = 833.3658
 1-4 NB = 319.1534 1-4 EEL = 3962.3669 VDWAALS = 6524.3781
 EELEC = -64764.9049 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4542.5932 VIRIAL = 4772.5128 VOLUME = 169291.9523
                                                Density = 1.0106
 Ewald error estimate: 0.3793E-05
 
------------------------------------------------------------------------------

 NSTEP = 6600 TIME(PS) = 4961.600 TEMP(K) = 301.29 PRESS = -49.2
 Etot = -41833.2442 EKtot = 10290.6459 EPtot = -52123.8901
 BOND = 267.5927 ANGLE = 737.1375 DIHED = 846.7068
 1-4 NB = 306.8492 1-4 EEL = 3970.7898 VDWAALS = 6561.6651
 EELEC = -64814.6312 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4571.9192 VIRIAL = 4751.6116 VOLUME = 169051.8821
                                                Density = 1.0120
 Ewald error estimate: 0.1122E-05
 
------------------------------------------------------------------------------

 NSTEP = 6700 TIME(PS) = 4961.700 TEMP(K) = 298.50 PRESS = 46.9
 Etot = -41839.1107 EKtot = 10195.6841 EPtot = -52034.7948
 BOND = 277.8845 ANGLE = 726.3443 DIHED = 835.6000
 1-4 NB = 304.5320 1-4 EEL = 3947.3038 VDWAALS = 6542.4171
 EELEC = -64668.8767 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4556.7967 VIRIAL = 4385.8516 VOLUME = 168938.1701
                                                Density = 1.0127
 Ewald error estimate: 0.4191E-05
 
------------------------------------------------------------------------------

 NSTEP = 6800 TIME(PS) = 4961.800 TEMP(K) = 298.80 PRESS = 124.4
 Etot = -41829.7811 EKtot = 10205.7771 EPtot = -52035.5582
 BOND = 271.2634 ANGLE = 714.7948 DIHED = 861.1520
 1-4 NB = 327.3404 1-4 EEL = 3973.7338 VDWAALS = 6593.3963
 EELEC = -64777.2389 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4580.3234 VIRIAL = 4126.4097 VOLUME = 168934.4775
                                                Density = 1.0127
 Ewald error estimate: 0.1744E-04
 
------------------------------------------------------------------------------

 NSTEP = 6900 TIME(PS) = 4961.900 TEMP(K) = 301.15 PRESS = -64.9
 Etot = -41820.1646 EKtot = 10286.1837 EPtot = -52106.3482
 BOND = 252.4161 ANGLE = 714.1134 DIHED = 859.9520
 1-4 NB = 324.1893 1-4 EEL = 3959.5846 VDWAALS = 6402.4153
 EELEC = -64619.0189 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4602.2684 VIRIAL = 4838.9847 VOLUME = 168968.4328
                                                Density = 1.0125
 Ewald error estimate: 0.4794E-05
 
------------------------------------------------------------------------------

check COM velocity, temp: 0.000000 0.00(Removed)

 NSTEP = 7000 TIME(PS) = 4962.000 TEMP(K) = 301.20 PRESS = 7.1
 Etot = -41815.3976 EKtot = 10287.7635 EPtot = -52103.1611
 BOND = 261.1966 ANGLE = 749.5415 DIHED = 862.3520
 1-4 NB = 314.4989 1-4 EEL = 3946.0642 VDWAALS = 6503.3912
 EELEC = -64740.2056 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4629.9481 VIRIAL = 4603.9726 VOLUME = 168945.3619
                                                Density = 1.0127
 Ewald error estimate: 0.8475E-05
 
------------------------------------------------------------------------------

 NSTEP = 7100 TIME(PS) = 4962.100 TEMP(K) = 299.29 PRESS = -44.3
 Etot = -41816.0813 EKtot = 10222.4834 EPtot = -52038.5648
 BOND = 265.0638 ANGLE = 714.7398 DIHED = 860.1382
 1-4 NB = 316.6735 1-4 EEL = 3940.3158 VDWAALS = 6528.1526
 EELEC = -64663.6485 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4517.6002 VIRIAL = 4678.9184 VOLUME = 168672.9438
                                                Density = 1.0143
 Ewald error estimate: 0.6403E-05
 
------------------------------------------------------------------------------

 NSTEP = 7200 TIME(PS) = 4962.200 TEMP(K) = 297.11 PRESS = 264.1
 Etot = -41819.3082 EKtot = 10147.8771 EPtot = -51967.1853
 BOND = 275.7279 ANGLE = 736.9878 DIHED = 855.7601
 1-4 NB = 305.4095 1-4 EEL = 3938.0708 VDWAALS = 6571.1477
 EELEC = -64650.2892 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 4569.6899 VIRIAL = 3608.3405 VOLUME = 168587.5174
                                                Density = 1.0148
 Ewald error estimate: 0.8551E-05
 
------------------------------------------------------------------------------

Cheers,

James.

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