> System size is 5 *5*3 nm when density reaches around 600 SI. Can you please > explain what do you mean by "What about dependence heat of evaporation vs > system size ?". I dont know how to compute vap. heat in gromacs!
1. Just use g_energy and compute potential energy. Then proceed by definition of Hvap. > Unfortunately, I am still unclear about energy units. :( > Yes, only when I use > g_energy -f ener.edr -o energy.xvg -nmol 8 I get pretty similar values > as you obtained (around 2200 KJ/molecule !? ) but then units should be > energy per molecule. I am confused because Before you had said units are per > mole. Without using -nmol 8 option total energy is around 20,000 (apparently > g_energy by default gives KJ/mole) 2. These are PER MOLE. Avogadro number is already included. Also see manual please. > Another reason I am confused is because > > g_energy -f ener.edr -o energy.xvg according to manual chapter 2 should give > energies in KJ/mol and not system. I did some simulations for different > number of polymer chains in a big box. (1, 2, 4, 8 chains). The magnitude of > energy values increase as number of chains increase..My question is if > values are in the units of KJ/mol why let's say nonbonded interaction energy > values are increasing in value as number of molecuels goes up? Should not > the values be the same if we are referring to MOLE number of molecules? 3. "g_energy" gives PER MOLE of the MD systems (unit cells). "g_energy -nmol XXX" gives PER MOLE of the molecules (XXX is the number of these molecules in system). Enjoy the polymer! Vitaly -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
