[gmx-users] Re: Heat of Vaporization

[Elisabeth]

On 3 August 2011 15:31, Dr. Vitaly V. Chaban <vvchaban at gmail.com> wrote:

> On Wed, Aug 3, 2011 at 3:17 PM, Elisabeth <katesedate at gmail.com> wrote:
> >
> >
> > On 2 August 2011 15:29, Dr. Vitaly V. Chaban <vvchaban at gmail.com> wrote:
> >>
> >> >
> >> > Hello,
> >> >
> >> > I wanted to know your ideas on calculation of heat of vaporization
> using
> >> > a
> >> > single phase run rather than running two separate simulations for
> liquid
> >> > and
> >> > gas!
> >> >
> >> > 1- Two separate simulations for liquid and gas
> >> >
> >> > DHvap = <Ugas> - <Uliq> + RT
> >> >
> >> > 1a: <total liquid potential> - <*total* potential of a single chain in
> >> > vacu
> >> >> ( bond+angle+torsion + nonbonded interaction of chain with itself)
> >> >
> >> > or
> >> >
> >> >  1b: *<total liquid potential> - < intra potential of a single chain
> in
> >> > vacu
> >> >> ( bond+angle+torsion) *
> >> >
> >> > 2- Single liquid phase run: (non need to run in vacu)
> >> >
> >> > 2a : DHvap = <total liquid potential> - < intra molecular potential
> >> > terms in
> >> > liquid phase> (same liquid phase simulation by adding up
> >> > bond+angle+torsion
> >> > terms)
> >> >
> >> > 2a: In other worlds *DHvap= <Uliq-nonbonded (vdw+electrostatics)> *
> >> >
> >> > In my case the latter definition is giving much more accurate results
> >> > than
> >> > 1a.
> >> >
> >> > I would like to know your idea and comments on methods 1b and 2a.
> >> >
> >> > Appreciate your comments.
> >> >
> >>
> >> What is your system?
> >>
> > system is liquid hydrocarbon polymer and 1a is giving inaccurate values.
> 2a
> > works far better but it seems not to be a common method.
>
>
> First of all, you should understand which particles exist in the vapor
> phase of your polymer. Notwithstanding the atomistic simulation. If
> this question is answered correctly, any method will provide you a
> decent result.
>
> I don't think that the whole "chains" of this polymer are flying in
> the vapor phase.....
>

Hello,

Thanks. I have only one single chain in vauo. pbc = no and cutoff is set to
zero for method 1a. Simulation runs for 20 ns and is equilibrated.

Best,
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