This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average or the
i
that's what i thought, and what i tried to do, my pressure is a bit higher
then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and
while I agree that gromacs is giving H as Etot + pV it appears that when i
calculate pV i get a different value from what g_energy returns for it I
>If you are computing enthaply in the NPT ensemble, P is constant, and
>is the applied pressure.
>The "pressure" quantity calculated from the KE and the virial is not
>the pressure. It is a quantity that when averaged over time is equal
>the pressure. Only the average is meaningful macroscop
>You should not use pV from g_energy though, as Michael explained, rather
>you need ref_p times . This precludes that your system is in
>equilibrium of course.
That is what I had initially thought, then take that with the to get
?
or should i be doing < U+*ref_p > = ?
But even so I still get d
> >or should i be doing < U+*ref_p > = ?
>More specifically, + *ref_p = H
> isn't really meaningful thing. I mean, you can define something
>such that = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk about this stuff, so thanks
for putting up with
or should i be doing < U+*ref_p > = ?
>>
>>> More specifically, + *ref_p = H
>>
>>> isn't really meaningful thing. I mean, you can define something
>>> such that = H, but that's not really thermodynamics.
>>
>> sorry I always have issues deciding how to talk about this stuff, so
>>
>Your calculation seems correct. Which gmx version did you use?
>The correlation between the numbers is almost 100% so there must be a
>simple explanation.
gmx version is 4.5.4, and yeah the correlation is odd, in the code you
listed:
>> pv = vol*md->ref_p/PRESFAC;
>>
>>
= 0
; Output frequency for pair distances to energy file
I've tried several things including pressurizing to 1000 bar then releasing it
to 1 bar and
have had no success.
Any suggestions would be much appreciated,
Jeffery Perkins
--
gmx-users mailing listgmx-users@gromacs.org
http://
his should be a good place to start looking,
best of luck,
Jeffery Perkins
-
Magdalena wrote:
Hi, i will be grateful for any clue.
Is it possible to extract an energy from finished trajectory? In my case the
trajectory wasn't leading with flag e so it'
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