in your mail: On 30 March 2011 15:30, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Elisabeth wrote: > >> Dear all, >> >> I intend to obtain vaporization heat per volume for a /pure alkane >> system/. Here is the steps I am taking. Please correct me. >> >> 1- Obtain total energy of system (kinetic+potential) and divide by number >> of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol >> XXX >> 2- Obtain total energy of a single molecule (use pbc). >> 3- Subtract step 2 from step 1. >> 4- Divide by simulation box volume. >> >> My questions is: >> >> in step 2 : what should be the box size? The same size as in 1 or it does >> not matter? (step 1 is done for the actual denstiy) >> >> > More troubling, how does one define the energy of a molecule? If you use > any sort of long-range algorithms (especially PME, but also dispersion > correction), you can't simply decompose the system like this. > > Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 > In the derivation of recent Gromos96 parameter sets, the heat of > vaporization is quite simple: > > DHvap = <Ugas> - <Uliq> + RT > 1- So <Uliq> is the total energy or only potential (no kinetic) 2- How can I compute <Ugas>? I have liquid now... > > Thank you, >> Regards, >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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/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 >
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