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

Braden Kelly bkelly08 at uoguelph.ca
Tue May 21 07:49:46 CEST 2019


Did you equilibrate the system? Typically you discard the initial values. You discard by adding "-b 200" to the gmx energy command line call. This doesn't include the first 200 Pico seconds in the averaging. 200 only is an example... I prefer more.

Another point is that you don't seem to have run for very long. I suggest plotting the potential energy and density of the system. You will know you have reached equilibrium  when they flatline around a value. Only include the values after equilibrium has been reached in you averaging.

Best of luck,


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From: Seketoulie Keretsu
Sent: Tuesday, May 21, 1:36 a.m.
Subject: [gmx-users] High pressure variation during NPT equilibration ofProtein-ligand system.
To: gromacs.org_gmx-users at maillist.sys.kth.se


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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.



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