[gmx-users] how to calculate the vaporation enthalpy of pure small organic compound

[David van der Spoel]

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
>> 　　　　　　　　wangjy at ciac.jl.cn
>> 　　　　　　　　　　2009-10-23
>>
>>
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>>
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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