[gmx-users] Re: NPT simulation

Vitaly Chaban vvchaban at gmail.com
Mon Aug 30 20:50:40 CEST 2010

> 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!


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