Jinyao Wang wrote:
Hi gmx-users,
I want to calcualted the the vaporation enthalpy of benzaldehyde
I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule.
So I made a NPT system simulation including 512 benzaldehyde molecule.
The following is the intermolecule nonbond interaction using the g_energy.
LJ-(SR)= -21128.7 Kj/mol
LJ-(LR)= -889.855 Kj/mol
Coulomb-(SR)= -3884.6 Kj/mol
Coul.-recip = -2261.51 Kj/mol
the sum of non-bond interaction = LJ-(SR) + LJ-(LR) + Coulomb-(SR) +
Coul.-recip = 28164.665 Kj/mol
But the experimental value of he vaporation enthalpy = 50.3 Kj/mol
I have no ideal that why they have so much different. Now I don't know how to
solve it.
Any suggestion will be appreciated.
These are totals for the intermolecular energy of the system. I'm guessing you
didn't use "-nmol 512" to calculate these results?
-Justin
This following is my md.mdp file.
title = fws
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 500000 ; total 1ns
nstcomm = 1
nstxout = 500
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1
tc_grps = system
ref_t = 298.15
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 2.0
compressibility = 4.6e-5
ref_p = 1.0
; Generate velocites is on at 323.15 K.
gen_vel = yes
gen_temp = 298.15
gen_seed = 173529
Jinyao Wang
[email protected]
2009-10-23
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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