AMBER Archive (2009)

Subject: Re: [AMBER] unexplained blow-up at restart

From: Sally Pias (sallypias_at_gmail.com)
Date: Fri Jul 10 2009 - 11:31:59 CDT

On Fri, Jul 10, 2009 at 9:29 AM, Sally Pias<sallypias_at_gmail.com> wrote:

> Below is the remainder of the run 2 output.  It looks like the
> restraint energy is already high after the first 500 steps.  I will
> see what other information I can gather.  (I will also look at the end
> of the heating phase, to see if there is anything obvious.)

I now realize that I was confused about what Carlos meant by run 2;
the output file in my most recent e-mail was for the previous run
(where the restraint energy was not high by comparison). Below is the
early output for the second NPT run, recording every step. For
brevity, I am including only the first 10 steps, but I have output for
1000, if we need them. The restraint energy is already VERY high on
the first step... I will now look in more detail at the energies but
wanted to correct myself first.

Sally

md2_NPT.out :
====
 NSTEP = 1 TIME(PS) = 160.001 TEMP(K) = 299.28 PRESS = -0.4
 Etot = 5987.2237 EKtot = 15346.7875 EPtot = -9359.5638
 BOND = 391.6012 ANGLE = 1125.3284 DIHED = 1420.6318
 1-4 NB = 449.0323 1-4 EEL = 3410.5202 VDWAALS = 9829.5268
 EELEC = -95078.1296 EHBOND = 0.0000 RESTRAINT = 69091.9251
 EAMBER (non-restraint) = -78451.4890
 EKCMT = 6923.3747 VIRIAL = 6925.4153 VOLUME = 256072.5778
                                                    Density = 1.0001
 Ewald error estimate: 0.9320E-04
 ------------------------------------------------------------------------------

 NSTEP = 2 TIME(PS) = 160.002 TEMP(K) = 303.82 PRESS = 26.6
 Etot = 5987.1564 EKtot = 15579.6808 EPtot = -9592.5245
 BOND = 388.8300 ANGLE = 1122.1154 DIHED = 1418.5791
 1-4 NB = 447.9170 1-4 EEL = 3416.7070 VDWAALS = 9834.2101
 EELEC = -95089.1771 EHBOND = 0.0000 RESTRAINT = 68868.2942
 EAMBER (non-restraint) = -78460.8186
 EKCMT = 6960.1525 VIRIAL = 6813.1393 VOLUME = 256072.5622
                                                    Density = 1.0001
 Ewald error estimate: 0.7086E-04
 ------------------------------------------------------------------------------

 NSTEP = 3 TIME(PS) = 160.003 TEMP(K) = 312.01 PRESS = 72.0
 Etot = 5987.1164 EKtot = 15999.6420 EPtot = -10012.5257
 BOND = 390.9713 ANGLE = 1142.3915 DIHED = 1417.9996
 1-4 NB = 447.6985 1-4 EEL = 3423.6340 VDWAALS = 9840.1745
 EELEC = -95101.0829 EHBOND = 0.0000 RESTRAINT = 68425.6878
 EAMBER (non-restraint) = -78438.2134
 EKCMT = 7078.5683 VIRIAL = 6680.6648 VOLUME = 256072.8544
                                                    Density = 1.0001
 Ewald error estimate: 0.7832E-04
 ------------------------------------------------------------------------------

 NSTEP = 4 TIME(PS) = 160.004 TEMP(K) = 322.69 PRESS = 134.2
 Etot = 5985.6660 EKtot = 16546.9700 EPtot = -10561.3040
 BOND = 396.5632 ANGLE = 1219.1729 DIHED = 1420.9979
 1-4 NB = 449.5186 1-4 EEL = 3430.4612 VDWAALS = 9847.9700
 EELEC = -95111.8622 EHBOND = 0.0000 RESTRAINT = 67785.8743
 EAMBER (non-restraint) = -78347.1784
 EKCMT = 7272.7093 VIRIAL = 6530.7047 VOLUME = 256073.6649
                                                    Density = 1.0001
 Ewald error estimate: 0.6468E-04
 ------------------------------------------------------------------------------

 NSTEP = 5 TIME(PS) = 160.005 TEMP(K) = 334.46 PRESS = 214.1
 Etot = 5978.3958 EKtot = 17150.7147 EPtot = -11172.3189
 BOND = 403.9179 ANGLE = 1383.1695 DIHED = 1430.3549
 1-4 NB = 454.5071 1-4 EEL = 3436.6362 VDWAALS = 9858.4523
 EELEC = -95118.6969 EHBOND = 0.0000 RESTRAINT = 66979.3401
 EAMBER (non-restraint) = -78151.6590
 EKCMT = 7546.2044 VIRIAL = 6362.1799 VOLUME = 256075.1862
                                                    Density = 1.0001
 Ewald error estimate: 0.9186E-04
 ------------------------------------------------------------------------------

 NSTEP = 6 TIME(PS) = 160.006 TEMP(K) = 346.44 PRESS = 307.3
 Etot = 5970.2578 EKtot = 17764.7552 EPtot = -11794.4974
 BOND = 410.1486 ANGLE = 1650.8559 DIHED = 1448.4805
 1-4 NB = 463.5501 1-4 EEL = 3441.5086 VDWAALS = 9871.5753
 EELEC = -95120.0480 EHBOND = 0.0000 RESTRAINT = 66039.4317
 EAMBER (non-restraint) = -77833.9291
 EKCMT = 7881.7838 VIRIAL = 6182.9337 VOLUME = 256077.6206
                                                    Density = 1.0001
 Ewald error estimate: 0.1052E-03
 ------------------------------------------------------------------------------

 NSTEP = 7 TIME(PS) = 160.007 TEMP(K) = 358.17 PRESS = 417.3
 Etot = 5966.1545 EKtot = 18366.2601 EPtot = -12400.1056
 BOND = 414.5055 ANGLE = 2011.5486 DIHED = 1477.3208
 1-4 NB = 476.7618 1-4 EEL = 3444.6643 VDWAALS = 9887.9345
 EELEC = -95114.9951 EHBOND = 0.0000 RESTRAINT = 65002.1540
 EAMBER (non-restraint) = -77402.2596
 EKCMT = 8297.3195 VIRIAL = 5989.9355 VOLUME = 256081.1184
                                                    Density = 1.0000
 Ewald error estimate: 0.6539E-04
 ------------------------------------------------------------------------------

 NSTEP = 8 TIME(PS) = 160.008 TEMP(K) = 369.53 PRESS = 545.2
 Etot = 5960.2781 EKtot = 18948.7003 EPtot = -12988.4222
 BOND = 418.1502 ANGLE = 2429.7673 DIHED = 1517.8304
 1-4 NB = 493.4587 1-4 EEL = 3445.9105 VDWAALS = 9907.4906
 EELEC = -95102.9722 EHBOND = 0.0000 RESTRAINT = 63901.9423
 EAMBER (non-restraint) = -76890.3645
 EKCMT = 8784.9317 VIRIAL = 5770.2363 VOLUME = 256085.8732
                                                    Density = 1.0000
 Ewald error estimate: 0.5707E-04
 ------------------------------------------------------------------------------

 NSTEP = 9 TIME(PS) = 160.009 TEMP(K) = 381.11 PRESS = 688.4
 Etot = 5957.8699 EKtot = 19542.9978 EPtot = -13585.1279
 BOND = 423.5867 ANGLE = 2850.1808 DIHED = 1569.6078
 1-4 NB = 512.2855 1-4 EEL = 3444.8736 VDWAALS = 9929.7254
 EELEC = -95085.4775 EHBOND = 0.0000 RESTRAINT = 62770.0897
 EAMBER (non-restraint) = -76355.2176
 EKCMT = 9332.5160 VIRIAL = 5525.8829 VOLUME = 256092.0891
                                                    Density = 1.0000
 Ewald error estimate: 0.6284E-04
 ------------------------------------------------------------------------------

 NSTEP = 10 TIME(PS) = 160.010 TEMP(K) = 393.49 PRESS = 852.3
 Etot = 5950.1544 EKtot = 20177.7843 EPtot = -14227.6299
 BOND = 434.8557 ANGLE = 3211.9215 DIHED = 1630.8781
 1-4 NB = 531.1804 1-4 EEL = 3441.9612 VDWAALS = 9953.4856
 EELEC = -95063.4816 EHBOND = 0.0000 RESTRAINT = 61631.5692
 EAMBER (non-restraint) = -75859.1991
 EKCMT = 9956.8468 VIRIAL = 5243.9786 VOLUME = 256099.9409
                                                    Density = 1.0000
 Ewald error estimate: 0.6572E-04
 ------------------------------------------------------------------------------

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