[gmx-users] High pressure variation during NPT equilibration of Protein-ligand system.

[David van der Spoel]

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