AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 10 2009 - 12:02:39 CDT

is the refc the same as for the first run? the restraint energy here should
be roughly comparable to the end of run 1, since you used the same mask.

On Fri, Jul 10, 2009 at 12:31 PM, Sally Pias <sallypias_at_gmail.com> wrote:

> 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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