Hi, I think that the best interpretation is that the energy is given as kJ per mole of simulation systems :)
Cheers, Tsjerk On Thu, Jan 7, 2010 at 8:42 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Cheong Wee Loong, Daniel wrote: >> >> Thanks Mark for your reply. >> >> So if I understand you correctly, it's not really a mole of anything in >> particular, it's just an energy value divided by Avogadro's number, and this >> happens to be consistent with the forcefield parameters as well. So if you >> have just a single molecule, that energy value is still divided by >> Avogadro's number. >> >> So if I were to take an interaction energy per unit area to estimate an >> interfacial energy, and I want to relate this to an experimental value given >> in dynes/cm, I would just need to multiply by Avogadro's number, in addition >> to all the other unit conversions (kJ/nm2 to dynes/cm), for the units to be >> consistent. Am I correct in my understanding? > > I think so. Whether such a quantity can be measured with an MM force field > might be another matter! > > Mark > >> -----Original Message----- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Mark Abraham >> Sent: Thursday, January 07, 2010 3:03 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Energy units >> >> Cheong Wee Loong, Daniel wrote: >>> >>> Hi all, >>> >>> >>> >>> This may be a silly and trivial question, but the energy unit given in >>> Gromacs is kJ/mol. What I don't quite understand is, the energy is per >>> mole of what exactly? >> >> In a very real sense, it doesn't matter. It's just a label for a >> convenient bucket of energy for chemistry. >> >> The energy of an isolated water molecule has a certain value, which we >> might measure in joules relative to some defined zero. Two such >> molecules at infinite separation would have twice that energy, etc. Once >> we start approaching Avogadro's number, we would prefer to express that >> energy as kJ/mol just for our numerical convenience. >> >> Equally, we could take a water molecule and a methane molecule at >> infinite separation, and add their energy... and add lots more... and >> get irritated at the size of the number, and just divide by Avogadro for >> convenience. The system is no longer homogeneous, but so long as we >> compare energies formed in the same way, our conclusions will be valid. >> >> MD force fields are typically parameterized against things like >> experimental or computational enthalpies of formation, normally measured >> in kJ/mol (unless you're a unlucky enough to be American!). So the >> parameters that get derived are conveniently measured in units derived >> from kJ/mol. We could convert them to "absolute" joules, but the numbers >> would all be stupid. There's a reason quantum chemists work in Hartrees! >> Were we to work in absolute joules, the numbers we'd produce then would >> still relate to the numbers we actually produce in kJ/mol - by Avogadro. >> >> Mark >> >>> The energy is system size dependent, so if I double the number of >>> molecules, the energy will double accordingly. But then the unit kJ/mol >>> seems to imply that it is size-independent. So how do I reconcile this? >>> >>> >>> >>> Also, let's say I have a protein molecule surrounded by water >>> molecules. Again in this case, I don't quite understand what "per mole" >>> means in this case. >>> >>> >>> >>> Thanks in advance for any insights you can teach me. >>> >>> >>> >>> Daniel >>> >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> This email is confidential and may be privileged. If you are not the >>> intended recipient, please delete it and notify us immediately. Please >>> do not copy or use it for any purpose, or disclose its contents to any >>> other person. Thank you. >>> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> >> This email is confidential and may be privileged. If you are not the >> intended recipient, please delete it and notify us immediately. Please do >> not copy or use it for any purpose, or disclose its contents to any other >> person. Thank you. > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php