[gmx-users] Re: Re: how to calculate the vaporation enthalpy of pure small organic compound (Justin A. Lemkul)

Jinyao Wang wangjy at ciac.jl.cn
Fri Oct 23 17:16:06 CEST 2009

```Dear Justin,
Thank you for your help. I indeed didn't use the option "-nmol 512".

>
>
>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
>>
>> ã€€ã€€ã€€ã€€ã€€ã€€ã€€
>>                ã€€Jinyao Wang
>> ã€€ã€€ã€€ã€€ã€€ã€€ã€€ã€€wangjy at ciac.jl.cn
>> ã€€ã€€ã€€ã€€ã€€ã€€ã€€ã€€ã€€ã€€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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>End of gmx-users Digest, Vol 66, Issue 157
>******************************************

= = = = = = = = = = = = = = = = = = = =

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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Jinyao Wang
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡wangjy at ciac.jl.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2009-10-23

```