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

[Justin A. Lemkul]

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