On Fri, Jun 21, 2013 at 4:23 PM, Ibrahim Said <saidibrahim569.gmail.com>wrote:
> 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,
>
You are looking at fluctuations over a small time scale (every 250 or 500
ps you take a sample, which is very frequent). When you look at
'converging' properties, you have to look/average over time scales longer
than the correlation time of that property.
You can use the script MdoutAnalyzer.py bundled with AmberTools 13 to
analyze the data in mdout files --- it also has an option to plot the
autocorrelation function of a dataset (like the density), so you can see
the time scale required for the density to decorrelate.
Also, the density fluctuations are quite small, and seems to go both up and
down -- I wouldn't claim to see any real trend in the density fluctuations
(although it's certainly not enough data to claim it's stabilized, either).
Why do you claim it hasn't stabilized?
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 21 2013 - 20:30:02 PDT
