[gmx-users] High pressure variation during NPT equilibration of Protein-ligand system.
Dallas Warren
dallas.warren at monash.edu
Tue May 21 23:42:16 CEST 2019
For some examples, see: https://twitter.com/dr_dbw/status/968624615063937025
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Tue, 21 May 2019 at 15:48, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Den 2019-05-21 kl. 07:36, skrev Seketoulie Keretsu:
> > Dear Experts,
> >
> > I am performing a protein-ligand stimulation in gromacs 2018. The
> > pressure value showed wild variation between -800 to 500 bar and
> > showed an average pressure value of -139 bar. The reference is 1 bar.
> > I have used the "lysozyme in water" simulation tutorial by Justin A.
> > Lemkul as a reference. The tutorial mentioned that 7.5 (+- 160) bar
> > was reasonable for the system. I'm not sure if the value I am getting
> > in my simulation results (-139 bar variation in pressure) are
> > reasonable. Kindly advise. How do i justify this ?
> >
> > References and suggestions will be appreciated. Thank you.
> This is normal. It will average out in a longer simulation. Larger boxes
> have less fluctuations in general.
>
> >
> > Regards,
> > Seketoulie
> >
> > Note: The pressure values from the NPT are given below:
> >
> > # This file was created Tue May 14 21:24:43 2019
> > # Created by:
> > # :-) GROMACS - gmx energy, 2018.4 (-:
> > #
> > # Executable: /usr/local/gromacs/bin/gmx
> > # Data prefix: /usr/local/gromacs
> > # Working dir: /home/biopo5/tutorial/Project4/JAK1/cmp49_jak1
> > # Command line:
> > # gmx energy -f nvt.edr -o pressure.xvg
> > # gmx energy is part of G R O M A C S:
> > #
> > # Gromacs Runs One Microsecond At Cannonball Speeds
> > #
> > @ title "GROMACS Energies"
> > @ xaxis label "Time (ps)"
> > @ yaxis label "(bar)"
> > @TYPE xy
> > @ view 0.15, 0.15, 0.75, 0.85
> > @ legend on
> > @ legend box on
> > @ legend loctype view
> > @ legend 0.78, 0.8
> > @ legend length 2
> > @ s0 legend "Pressure"
> > 0.000000 -3931.674805
> > 1.000000 528.706482
> > 2.000000 27.634497
> > 3.000000 -130.418900
> > 4.000000 -491.462982
> > 5.000000 3.087336
> > 6.000000 -246.631638
> > 7.000000 -86.932167
> > 8.000000 -453.551422
> > 9.000000 -46.325455
> > 10.000000 270.657562
> > 11.000000 -432.105682
> > 12.000000 -578.059326
> > 13.000000 -397.159760
> > 14.000000 180.598190
> > 15.000000 -159.344788
> > 16.000000 -122.911415
> > 17.000000 470.059418
> > 18.000000 -375.501251
> > 19.000000 -310.881561
> > 20.000000 68.639618
> > 21.000000 157.454422
> > 22.000000 -619.447388
> > 23.000000 -130.864059
> > 24.000000 58.016773
> > 25.000000 -132.054276
> > 26.000000 114.288574
> > 27.000000 -108.022186
> > 28.000000 -235.894424
> > 29.000000 -398.703217
> > 30.000000 252.965332
> > 31.000000 -269.996368
> > 32.000000 -58.096252
> > 33.000000 -291.578918
> > 34.000000 15.896652
> > 35.000000 53.429890
> > 36.000000 43.522858
> > 37.000000 -442.695190
> > 38.000000 111.608665
> > 39.000000 -12.626378
> > 40.000000 -136.936111
> > 41.000000 182.577164
> > 42.000000 -68.747620
> > 43.000000 121.546547
> > 44.000000 127.403526
> > 45.000000 -248.055176
> > 46.000000 184.869797
> > 47.000000 162.962906
> > 48.000000 -387.420013
> > 49.000000 228.167648
> > 50.000000 348.351471
> > 51.000000 -462.909180
> > 52.000000 -234.574936
> > 53.000000 -224.565689
> > 54.000000 311.879456
> > 55.000000 -404.242920
> > 56.000000 -740.461182
> > 57.000000 38.036850
> > 58.000000 -677.158447
> > 59.000000 -117.842407
> > 60.000000 -20.302151
> > 61.000000 -558.201233
> > 62.000000 218.174881
> > 63.000000 -269.575531
> > 64.000000 -153.398697
> > 65.000000 178.027954
> > 66.000000 -193.050797
> > 67.000000 -590.598694
> > 68.000000 -487.503754
> > 69.000000 171.980606
> > 70.000000 84.821785
> > 71.000000 -219.844803
> > 72.000000 -228.680954
> > 73.000000 -145.632614
> > 74.000000 47.675121
> > 75.000000 -310.033478
> > 76.000000 -705.341248
> > 77.000000 212.275406
> > 78.000000 24.035654
> > 79.000000 -221.810410
> > 80.000000 -189.725708
> > 81.000000 217.696289
> > 82.000000 427.632660
> > 83.000000 249.210770
> > 84.000000 -405.385956
> > 85.000000 78.898247
> > 86.000000 -19.268747
> > 87.000000 85.342247
> > 88.000000 155.808731
> > 89.000000 2.646250
> > 90.000000 -284.466888
> > 91.000000 152.030930
> > 92.000000 280.804352
> > 93.000000 -182.475830
> > 94.000000 -268.784149
> > 95.000000 -470.018829
> > 96.000000 -163.642685
> > 97.000000 291.026855
> > 98.000000 -982.940430
> > 99.000000 155.447800
> > 100.000000 77.415077
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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