# How is the enthalpy computed in gromacs? **URL:** \ **Category:** User discussions\ **Created:** [April 21, 2024, 10:19pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949 "2024-04-21T22:19:59Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Julio1200](https://avatars.discourse-cdn.com/v4/letter/j/b782af/32.png) [@Julio1200](https://gromacs.bioexcel.eu/u/Julio1200)\ **Post date:** [April 21, 2024, 10:19pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/1 "2024-04-21T22:19:59Z")
GROMACS version: 2021.4-2 GROMACS modification: Yes/No Hello, I’m trying to run MD simulations of liquid propanol in the NPT ensemble, and I’m a bit confused about my results. After the simulation, I computed the thermodynamic proprieties below using gmx energy: ## Energy Average Err.Est. RMSD Tot-Drift Potential -20.5116 0.84 2.40346 -4.75479 (kJ/mol) Total Energy 14.1659 0.84 2.42722 -4.66579 (kJ/mol) Temperature 298.024 0.16 3.71291 0.764872 (K) Pressure -13.653 11 401.47 0.0591182 (bar) Volume 62.8428 0.47 1.26078 -2.81342 (nm^3) Density 794.311 5.8 15.1766 34.2912 (kg/m^3) Enthalpy 7086.76 420 1213.68 -2333.07 (kJ/mol) The enthalpy is much larger than the total energy and the potential energy, and I would like why. Furthermore, gromacs also computed other thermodynamics properties, that are printed below: Volume = 7.56896e-05 m^3/mol Enthalpy = 14.1735 kJ/mol Coefficient of Thermal Expansion Alpha\_P = 0.0289423 (1/K) Isothermal Compressibility Kappa = 6.14731e-09 (m^3/J) Adiabatic bulk modulus = 1.62673e+08 (J/m^3) Heat capacity at constant pressure Cp = 3989.33 J/(mol K) Cp-Cv = 3073.76 J/(mol K) Now the enthalpy appear again, but with a very different value. Why there are two enthapies in gromacs? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [April 23, 2024, 2:12pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/2 "2024-04-23T14:12:34Z")
That looks strange. Do you get the same with a supported version of GROMACS? You say that you calculated the values in the upper table using `gmx energy`. How did you calculate the values below? ---
**Author:** ![Julio1200](https://avatars.discourse-cdn.com/v4/letter/j/b782af/32.png) [@Julio1200](https://gromacs.bioexcel.eu/u/Julio1200)\ **Post date:** [April 23, 2024, 10:13pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/3 "2024-04-23T22:13:05Z")
Hi MagnusL. What would be a supported version? The values below were computed also with gmx energy. When I use gmx energy, gromacs automatically compute all these values. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [April 24, 2024, 6:27am UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/4 "2024-04-24T06:27:34Z")
2023 and 2024 are supported, see [https://manual.gromacs.org/current/release-notes/index.html](https://manual.gromacs.org/current/release-notes/index.html) for more information. Thanks for the clarification. But I still don’t understand fully. I don’t think `gmx energy` calculates anything automatically. And it looks strange that there are two volume and enthalpy outputs. Could you copy and paste the `gmx energy` command you are running, all output from the command (i.e. what observables you can choose from), the observables you choose to analyse as well as the results from the command? ---
**Author:** ![Julio1200](https://avatars.discourse-cdn.com/v4/letter/j/b782af/32.png) [@Julio1200](https://gromacs.bioexcel.eu/u/Julio1200)\ **Post date:** [April 24, 2024, 9:04am UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/5 "2024-04-24T09:04:35Z")
Thanks, I will try to install the latest version of gromacs and run again. To comando I used was gmx energy -f md.edr -fluct\_props -nmol 500 -o prop\_md.xvg and I selected potencial, temperature, total-energy, density, enthalpy, volume and pressure. The output was (it’s a bit different because it’s another test, but the problem continue): ``` :-) GROMACS - gmx energy, 2021.4-Ubuntu-2021.4-2 (-: GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel ``` Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx energy, version 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/leonardo/Desktop/doutorado/Calc\_propanol/MD\_propanol\_liquido Command line: gmx energy -f md.edr -fluct\_props -nmol 500 -o prop\_md.xvg Opened md.edr as single precision energy file ## Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. 1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 13 Conserved-En. 14 Temperature 15 Pres.-DC 16 Pressure 17 Constr.-rmsd 18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf\*SurfTen 44 T-System 45 Lamb-System Last energy frame read 5000 time 1000.000 Statistics over 500001 steps [0.0000 through 1000.0000 ps], 7 data sets All statistics are over 5001 points (frames) ## Energy Average Err.Est. RMSD Tot-Drift Potential -20.1634 0.031 0.509918 0.16298 (kJ/mol) Total Energy 14.525 0.031 0.659254 0.160342 (kJ/mol) Temperature 298.068 0.03 3.43175 -0.0226725 (K) Pressure 6.17727 10 392.094 -53.3204 (bar) Volume 62.7184 0.02 0.269243 0.0483782 (nm^3) Density 795.568 0.25 3.41745 -0.609909 (kg/m^3) Enthalpy 7266.29 15 329.632 80.1737 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! Temperature dependent fluctuation properties at T = 298.068. Heat capacities obtained from fluctuations do _not_ include quantum corrections. If you want to get a more accurate estimate please use the g\_dos program. WARNING: Please verify that your simulations are converged and perform a block-averaging error analysis (not implemented in g\_energy yet) Volume = 7.55398e-05 m^3/mol Enthalpy = 14.5326 kJ/mol Coefficient of Thermal Expansion Alpha\_P = 0.000594451 (1/K) Isothermal Compressibility Kappa = 2.80862e-10 (m^3/J) Adiabatic bulk modulus = 3.56046e+09 (J/m^3) Heat capacity at constant pressure Cp = 294.188 J/(mol K) Cp-Cv = 28.3289 J/(mol K) ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. P. Allen and D. J. Tildesley Computer simulation of liquids Oxford Science Publications 1 (1987) pp. 1 -------- -------- — Thank You — -------- -------- ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [April 24, 2024, 1:24pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/6 "2024-04-24T13:24:36Z")
I can reproduce the error in GROMACS 2021.4, but it works fine in version 2022 (at least from version 2022.3). The problem seems to be inconsistent treatment of -nmol. ---
**Author:** ![Julio1200](https://avatars.discourse-cdn.com/v4/letter/j/b782af/32.png) [@Julio1200](https://gromacs.bioexcel.eu/u/Julio1200)\ **Post date:** [April 25, 2024, 11:37am UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/7 "2024-04-25T11:37:41Z")
I installed 2024.1 and run the simulation, and it worked also! There is no more inconsistencies. Now I will use this version of gromacs. Thank you so much! ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [April 25, 2024, 12:53pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/8 "2024-04-25T12:53:39Z")
Good to hear it’s working. I should I have been clearer, though. You don’t need to rerun the simulations. It’s only the analysis that is different (in this specific aspect). ---
**Author:** ![Julio1200](https://avatars.discourse-cdn.com/v4/letter/j/b782af/32.png) [@Julio1200](https://gromacs.bioexcel.eu/u/Julio1200)\ **Post date:** [April 25, 2024, 9:26pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/9 "2024-04-25T21:26:24Z")
ah ok, thanks again! ---
**Author:** ![dspoel](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dspoel/32/64_2.png) [@dspoel](https://gromacs.bioexcel.eu/u/dspoel)\ **Post date:** [April 12, 2025, 8:10pm UTC](https://gromacs.bioexcel.eu/t/how-is-the-enthalpy-computed-in-gromacs/8949/10 "2025-04-12T20:10:53Z")
Unfortunately I the code for computing the fluctuations is not correct. This has been broken for a long time, at least since 4.6.7. I started reimplementing this code long ago and Mark Abraham worked on it as well, but my new code never made it into official gromacs. I happened to stumble over these problems when I tried to calculates alpha\_P and kappa\_T.