Elisabeth wrote:
On 31 March 2011 12:58, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure
alkane system/. Here is the steps I am taking. Please
correct me.
1- Obtain total energy of system (kinetic+potential) and
divide
by number of molecules to obtain energy per mol of molecules.
g_energy -f *.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.
My questions is:
in step 2 : what should be the box size? The same size as
in 1
or it does not matter? (step 1 is done for the actual
denstiy)
More troubling, how does one define the energy of a molecule? If
you use any sort of long-range algorithms (especially PME,
but also
dispersion correction), you can't simply decompose the system
like this.
Thanks Justin and David.
I have been trying to find the article in which this has been
presented. If you have time Please see page 5937, right column,
equation 11. I think I made a mistake and I dont have to include
kinetic energy, Only nonboded energies!?
http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539
What is cohesive energy and how does it relate to the quantity
you're trying to calculate?
It is delta Hvap/volume. It is directly related to Hvap. What is
happening is that they are calculating nonbonded energy of some
chains, divide by number of chains and substract from nonbonded
energy of a single chain in vacuum. These are the steps I wrote in
my first post but I think I should not have included kinetic and
should just look at LJ-SR and Coulomb-SR.
I am using PME..If I remember correctly LR is included in Coulomb-SR and
can not get decomposed? But I dont think this doesnt matter since if I
am to take nonbonded energies this should not hurt,,,
Please comment ...
PME energies are from nonbonded interactions. The mesh energy is written to the
"Coul-recip" term in the .edr file. If there is some other "Coul (LR)" term, it
is because you're using a twin-range cutoff such that rcoulomb > rlist, which I
do not believe is correct when using PME.
In the derivation of recent Gromos96 parameter sets, the heat of
vaporization is quite simple:
DHvap = <Ugas> - <Uliq> + RT
1- So <Uliq> is the total energy or only potential (no kinetic)
Potential.
2- How can I compute <Ugas>? I have liquid now...
Run a simulation in the gas phase.
Sorry, but how can I do this? :( I have box of molecules with density of
actual liquid..How can I shift to gas phase ..I mean how many molecules
I need to keep in the box..
Make a box with an equivalent number of molecules separated by some large amount
of space (i.e. 50 nm or so). Set pbc=no and all cutoffs to zero. I'm basing
this on Gromos96 parameterization, but I don't know what your target force field is.
-Justin
Many thanks...
-Justin
Thank you,
Regards,
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
