[gmx-users] Re: Heat of Vaporization

[Dr. Vitaly V. Chaban]

I wonder how you know that your polymer chain in computer is exactly
your polymer chain in experiment.... Of course, the difference of
vaporazation enthalpy per mole is to be observed. You may guess, may
not guess, but method is not guilty if you may not.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA




On Wed, Aug 3, 2011 at 4:37 PM, Elisabeth <katesedate at gmail.com> wrote:
>
>
> 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,
>
>