Re: [gmx-users] how to calculate the vaporation enthalpy of pure small organic compound
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 = 50 ; 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 wan...@ciac.jl.cn 2009-10-23 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to calculate the vaporation enthalpy of pure small organic compound
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 = 50 ; 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 wan...@ciac.jl.cn 2009-10-23 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to calculate the vaporation enthalpy of pure small organic compound
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. This following is my md.mdp file. title = fws cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 50 ; 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 wan...@ciac.jl.cn 2009-10-23 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
