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

[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.

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