[gmx-users] how to calculate the vaporation enthalpy of pure small organic compound
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 23 16:52:26 CEST 2009
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.
>> 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
>> wangjy at ciac.jl.cn
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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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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