Re: AMBER: problems with pmemd from Robert Duke on 2003-08-22 (Amber Archive Aug 2003)

From: Robert Duke <rduke.email.unc.edu>
Date: Fri, 22 Aug 2003 12:45:47 -0400

James -
Well, the pmemd simulation clearly blew up. This is most probably related
to your earlier problems with not wrapping the coordinates, but why pmemd is
responding differently, I am not sure. First of all, are you using pmemd in
amber 7 compatibility mode? The reason I ask is that in sander 7 there is a
default vlimit of 10 (I think), as opposed to no default vlimit in sander 6.
Pmemd does not use a vlimit in 6-mode, but mimics sander 7's treatment of
vlimits in 7 mode. I presume that nscm/ntcm are okay, based on COM printout
in the listing below, but the fact you suddenly have significant COM removal
indicates the pmemd simulation is in trouble. I really need to have a look
at all the input files for both these runs, and information or inputs for
earlier phases of the simulation would be useful. If there really is a bug
in pmemd, I WANT to get it fixed immediately. The last thing in the world I
want is nebulous reports of strange behaviour that may or may not be related
to the simulation instead of the software. Once the system starts
expanding, I am not at all surprised that things go south in a hurry. I am
not sure how several data structures would respond to a significant increase
in the unit cell size; in normal simulations, presuming we are not doing
bomb blasts, this doesn't happen. Anyway, it is interesting, and I want to
get to the bottom of it, so please send the files.
Regards - Bob

----- Original Message -----
From: "james tomomi macdonald" <j.macdonald.mail.cryst.bbk.ac.uk>
To: <amber.scripps.edu>
Sent: Friday, August 22, 2003 11:37 AM
Subject: AMBER: problems with pmemd

>
> 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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Received on Fri Aug 22 2003 - 17:53:00 PDT