Justin A. Lemkul wrote:
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?
And then subtract the gas-phase energy (with com removed) and add kT.
-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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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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