On 31 March 2011 12:58, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Elisabeth wrote: > >> >> >> in your mail: >> >> >> On 30 March 2011 15:30, Justin A. Lemkul <jalem...@vt.edu <mailto: >> 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 >> >> > What is cohesive energy and how does it relate to the quantity you're > trying to calculate? > > It is delta Hvap/volume. It is directly related to Hvap. What is happening > is that they are calculating nonbonded energy of some chains, divide by > number of chains and substract from nonbonded energy of a single chain in > vacuum. These are the steps I wrote in my first post but I think I should > not have included kinetic and should just look at LJ-SR and Coulomb-SR. >
I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... > >> 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) >> > > Potential. > > > 2- How can I compute <Ugas>? I have liquid now... >> >> > Run a simulation in the gas phase. > Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Many thanks... > > -Justin > > >> 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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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