[gmx-users] Re: Enthalpy Confusion
or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy Here's the code: /* This is pV (in kJ/mol). The pressure is the reference pressure, not the instantaneous pressure */ pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT]; What is your volume? What is Etot? a bit messy but this is data from g_energy for the system with increasing temperature (300 K-1000 K), and constant pressure of 1000 bar (so 100 000 000 Pascals): Temperature VolumeEnthalpy Potential Total EnergypV Kinetic En. K nm^3 kJ/molkJ/mol kJ/mol kJ/mol kJ/mol 299.914 14.7226 -1168.83 -2565.44-1611.63442.791 953.817 399.901 17.462 -339.795 -2080.31-808.501468.706 1271.81 499.898 21.0263 421.763 -1666.7 -76.8794498.643 1589.83 599.899 25.1149 1088.79 -1348.14559.718 529.07 1907.86 699.914 29.4219 1668.2-1115.471110.46 557.733 2225.94 799.925 33.7642184.31 -943.6131600.39 583.922 2544 899.923 38.0865 2660.3 -809.5722052.45 607.847 2862.03 999.931 42.2798 3101.56-707.9082472.17 629.383 3180.08 all uncorrected for the number of particles in the box (so Etot is in kJ/256 mol of particles) when i use this data to get H myself i get: H kJ/mol -725.32948 242.7114 1188.90386 2071.63498 2881.65838 3632.9828 4345.2573 5017.41396 again uncorrected for the number of particles in the box Thoughts? -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009164.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-14 19:28, Jeffery Perkins wrote: or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy Here's the code: /* This is pV (in kJ/mol). The pressure is the reference pressure, not the instantaneous pressure */ pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT]; What is your volume? What is Etot? a bit messy but this is data from g_energy for the system with increasing temperature (300 K-1000 K), and constant pressure of 1000 bar (so 100 000 000 Pascals): Temperature VolumeEnthalpy Potential Total EnergypV Kinetic En. K nm^3 kJ/molkJ/mol kJ/mol kJ/mol kJ/mol 299.914 14.7226 -1168.83 -2565.44-1611.63442.791 953.817 399.901 17.462 -339.795 -2080.31-808.501468.706 1271.81 499.898 21.0263 421.763 -1666.7 -76.8794498.643 1589.83 599.899 25.1149 1088.79 -1348.14559.718 529.07 1907.86 699.914 29.4219 1668.2-1115.471110.46 557.733 2225.94 799.925 33.7642184.31 -943.6131600.39 583.922 2544 899.923 38.0865 2660.3 -809.5722052.45 607.847 2862.03 999.931 42.2798 3101.56-707.9082472.17 629.383 3180.08 all uncorrected for the number of particles in the box (so Etot is in kJ/256 mol of particles) when i use this data to get H myself i get: H kJ/mol -725.32948 242.7114 1188.90386 2071.63498 2881.65838 3632.9828 4345.2573 5017.41396 again uncorrected for the number of particles in the box Thoughts? Your calculation seems correct. Which gmx version did you use? The correlation between the numbers is almost 100% so there must be a simple explanation. -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009164.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Enthalpy Confusion
Your calculation seems correct. Which gmx version did you use? The correlation between the numbers is almost 100% so there must be a simple explanation. gmx version is 4.5.4, and yeah the correlation is odd, in the code you listed: pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT] so pv = vol * md-ref_p/PRESFAC; is the vol * ref_p/conversion factor, right? the only thing there that seems like it could be off is if PRESFAC isn't correct for some reason (correct me if I'm wrong of course!) Jeffery -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009168.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-14 21:39, Jeffery Perkins wrote: Your calculation seems correct. Which gmx version did you use? The correlation between the numbers is almost 100% so there must be a simple explanation. gmx version is 4.5.4, and yeah the correlation is odd, in the code you listed: Then that is the reason. I forgot about it, but the calculation of pv is incorrect in that version. If you use 4.5.7 or 4.6.2 it should be fine. pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT] so pv = vol * md-ref_p/PRESFAC; is the vol * ref_p/conversion factor, right? the only thing there that seems like it could be off is if PRESFAC isn't correct for some reason (correct me if I'm wrong of course!) Jeffery -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009168.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-11 23:31, Jeffery Perkins wrote: or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy Here's the code: /* This is pV (in kJ/mol). The pressure is the reference pressure, not the instantaneous pressure */ pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT]; What is your volume? What is Etot? PRESFAC ~ 16.6 -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009068.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Enthalpy Confusion
that's what i thought, and what i tried to do, my pressure is a bit higher then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and while I agree that gromacs is giving H as Etot + pV it appears that when i calculate pV i get a different value from what g_energy returns for it I did p in Pa, V in m^3, as the whole box, to get J of energy, and then multiply by 6.02E23 to get J/mol of my box, and then convert down to kJ/mol to be the same units as g_energy. When you say the applied pressure you mean that p = ref_p? or the calculated pressure from the virial and Ke? Thanks for the help, Jeffery -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009058.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Enthalpy Confusion
If you are computing enthaply in the NPT ensemble, P is constant, and is the applied pressure. The pressure quantity calculated from the KE and the virial is not the pressure. It is a quantity that when averaged over time is equal the pressure. Only the average is meaningful macroscopically. If you are computing enthalpy in another ensemble (which is possible, though it may be harder to interpret) then you would use the average pressure from this quantity. On Tue, Jun 11, 2013 at 3:08 PM, Jeffery Perkins jeffery.perk...@ufv.ca wrote: that's what i thought, and what i tried to do, my pressure is a bit higher then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and while I agree that gromacs is giving H as Etot + pV it appears that when i calculate pV i get a different value from what g_energy returns for it I did p in Pa, V in m^3, as the whole box, to get J of energy, and then multiply by 6.02E23 to get J/mol of my box, and then convert down to kJ/mol to be the same units as g_energy. When you say the applied pressure you mean that p = ref_p? or the calculated pressure from the virial and Ke? Thanks for the help, Jeffery -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009058.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Enthalpy Confusion
If you are computing enthaply in the NPT ensemble, P is constant, and is the applied pressure. The pressure quantity calculated from the KE and the virial is not the pressure. It is a quantity that when averaged over time is equal the pressure. Only the average is meaningful macroscopically. Right, that's an easy one to miss but i don't think that's my problem here. If you are computing enthalpy in another ensemble (which is possible, though it may be harder to interpret) then you would use the average pressure from this quantity I'm running in NPT and was calcaulating H from ave. P, ave. U and ave. V for the run while i understand that this doesn't exactly equal average H it should be close enough for me at this point, going back and redoing it with P set to the reference value (which the average hits with small fluctuations) the resultant H still doesn't line up properly for some example data: pV, g_energyV, m^3 pV, J pV, kJ/mol 442.42 1.46E-26 1.46E-18884.07 P = 1000 bar = 100,000,000 Pa and i see that my pV is around 2x g_energies pV, no values are scaled for the # of items in the box at this point, this is all for moles of the system i think that's alright though -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009062.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-11 21:57, Jeffery Perkins wrote: If you are computing enthaply in the NPT ensemble, P is constant, and is the applied pressure. The pressure quantity calculated from the KE and the virial is not the pressure. It is a quantity that when averaged over time is equal the pressure. Only the average is meaningful macroscopically. Right, that's an easy one to miss but i don't think that's my problem here. If you are computing enthalpy in another ensemble (which is possible, though it may be harder to interpret) then you would use the average pressure from this quantity I'm running in NPT and was calcaulating H from ave. P, ave. U and ave. V for the run while i understand that this doesn't exactly equal average H it should be close enough for me at this point, going back and redoing it with P set to the reference value (which the average hits with small fluctuations) the resultant H still doesn't line up properly for some example data: pV, g_energyV, m^3 pV, J pV, kJ/mol 442.42 1.46E-26 1.46E-18884.07 P = 1000 bar = 100,000,000 Pa and i see that my pV is around 2x g_energies pV, no values are scaled for the # of items in the box at this point, this is all for moles of the system i think that's alright though You should not use pV from g_energy though, as Michael explained, rather you need ref_p times V. This precludes that your system is in equilibrium of course. -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009062.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Enthalpy Confusion
You should not use pV from g_energy though, as Michael explained, rather you need ref_p times V. This precludes that your system is in equilibrium of course. That is what I had initially thought, then take that with the U to get H? or should i be doing U+V*ref_p = H? But even so I still get different values for H then g_energy returns example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either way I was mostly using pV as a stand in for H as it seems to be where the difference between manual calculation and g_energy lies thanks again for taking the time to assist, Jeffery -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Enthalpy Confusion
or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Enthalpy Confusion
or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009068.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
