Re: [gmx-users] Heat of vap
On 2011-04-04 01.32, Justin A. Lemkul wrote: Elisabeth wrote: Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: To get heat of vaporization, you shouldn't be simulating just a single molecule in the gas phase, it should be an equivalent number of molecules as you have in the liquid phase. Hello David and Justin, My explanation was not clear. Below is the results for liquid phase and for gas phase I tried two cases: one single molecule and the other time for equivalent number of molecules as in liquid phase and thats why results are very similar. ( However Justin says one single molecule is not correct. I think when cutoffs is set to zero only bonded terms are What is not correct is comparing the potential energy of a liquid system of many molecules with a gas phase of a single molecule. Whether or not that was something you did still is not entirely clear, but to be very clear, that's what I was saying is incorrect to do. DHvap is based on conversion of equivalent systems between liquid and gas. treated and even where there are many particles in gas phase to get This is incorrect. Cutoffs of zero mean that all nonbonded interactions are calculated, they are not truncated. energies per mole of molecules i.e g_energy -nmol XXX must be used so values should be colse to a single molecules case.. please correct me! Anyway results for gas phase are close and this is not the issue now). You shouldn't need -nmol for any of this. Simply take the potential energy of the two systems (with equivalent numbers of molecules) and apply the formula I gave you several emails ago. NOO 1 molecule in the gas phase - Epot(g) in your case 59.2 kJ/mol N molecules in the liquid phase - Epot(l) (since this is per mole you DO need the -nmol option) in you case 34.7 kJ/mol DHvap = Epot(g) + kBT - Epot(l) = 59.2+2.5-34.7 = 27 kJ/mol which is quite close to hexane (28.9 kJ/mol). -Justin Liquid phase: Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR) -27.3083 0.01 0.296591 -0.0389173 (kJ/mol) Coulomb (SR) 6.00527 0.0074 0.122878 0.00576827 (kJ/mol) Coul. recip. 5.59559 0.0032 0.0557413 0.00316957 (kJ/mol) Potential *34.6779 * 0.025 1.03468 -0.11177 (kJ/mol) Total Energy 86.4044 0.026 1.44353 -0.112587 (kJ/mol) *one single molecule in gas phase* Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR) -2.24473 0.073 1.292 0.342696 (kJ/mol) Coulomb (SR) 11.5723 0.55 2.17577 -2.33224 (kJ/mol) Potential * 59.244 * 0.94 10.9756 6.35631 (kJ/mol) Total Energy 106.647 1 15.4828 6.78792 (kJ/mol) *equivalent number of molecules as in liquid* ( large box 20 nm) Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR) -2.16367 0.053 0.171542 0.374027 (kJ/mol) Coulomb (SR) 11.2894 0.23 0.49105 -1.44437 (kJ/mol) Potential * 63.2369 * 1.1 2.47211 7.69756 (kJ/mol) Total Energy 114.337 1.1 2.65547 7.72258 (kJ/mol) Since pbc is set to NO molecules leave the box and I dont know if this all right. I hope the difference is acceptable...! For pbc = no there is no box. 0- I am going to do the same calculation but for some polymers solvated in the alkane. For binary system do I need to look at nonboded terms? and then run a simulation for a single polymer in vacuum? Can you please provide me with a recipe for Delta Hvap of the solute in a solvent? The method for calculating heat of vaporization is not dependent upon the contents of the system; it is a fundamental thermodynamic definition. Heat of vaporization is not something that can be calculated from a solute in a solvent. You can calculate DHvap for a particular system, but not some subset of that system. Thanks Justin. I am interested in the energy required to vaporize the solute in a particular solvent not the whole DHvap of the mixture. do you think this can be achieved by calculating nonbonded energies between solute and solvent? ( defining energy groups ..) 1- If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? The PME-related terms contain both solute-solvent, solvent-solvent, and potentially solute-solute terms (depending on the size and nature of the solute), so trying to interpret this term in some pairwise fashion is an exercise in futility. What you mean is when one uses PME interaction energies between components can not be decomposed? So the energy groups I defined to extract nonbonded energies are not giving
Re: [gmx-users] Heat of vap
On 2011-04-03 02.15, Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: *one single molecule in gas phase* Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.24473 0.073 1.292 0.342696 (kJ/mol) Coulomb (SR)11.5723 0.552.17577 -2.33224 (kJ/mol) Potential * 59.244 * 0.9410.97566.35631 (kJ/mol) Total Energy106.647 115.48286.78792 (kJ/mol) *equivalent number of molecules as in liquid* ( large box 20 nm) This is not correct. You need to simulate the liquid in the liquid state. Now you have a dilute gas instead, hence the energy difference is very small and due to dimers and trimers in the gas phase. Just extract Epot from your previous liquid phase calculations. Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.16367 0.053 0.171542 0.374027 (kJ/mol) Coulomb (SR)11.2894 0.230.49105 -1.44437 (kJ/mol) Potential * 63.2369 *1.12.472117.69756 (kJ/mol) Total Energy114.3371.12.655477.72258 (kJ/mol) Since pbc is set to NO molecules leave the box and I dont know if this all right. I hope the difference is acceptable...! 0- I am going to do the same calculation but for some polymers solvated in the alkane. For binary system do I need to look at nonboded terms? and then run a simulation for a single polymer in vacuum? Can you please provide me with a recipe for Delta Hvap of the solute in a solvent? 1- If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.0 ff: OPLSAA Appreciate your help, Best, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: To get heat of vaporization, you shouldn't be simulating just a single molecule in the gas phase, it should be an equivalent number of molecules as you have in the liquid phase. Hello David and Justin, My explanation was not clear. Below is the results for liquid phase and for gas phase I tried two cases: one single molecule and the other time for equivalent number of molecules as in liquid phase and thats why results are very similar. ( However Justin says one single molecule is not correct. I think when cutoffs is set to zero only bonded terms are treated and even where there are many particles in gas phase to get energies per mole of molecules i.e g_energy -nmol XXX must be used so values should be colse to a single molecules case.. please correct me! Anyway results for gas phase are close and this is not the issue now). Liquid phase: Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-27.3083 0.01 0.296591 -0.0389173 (kJ/mol) Coulomb (SR)6.00527 0.0074 0.122878 0.00576827 (kJ/mol) Coul. recip.5.59559 0.0032 0.0557413 0.00316957 (kJ/mol) Potential *34.6779 *0.0251.03468 -0.11177 (kJ/mol) Total Energy86.4044 0.0261.44353 -0.112587 (kJ/mol) *one single molecule in gas phase* Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.24473 0.073 1.292 0.342696 (kJ/mol) Coulomb (SR)11.5723 0.552.17577 -2.33224 (kJ/mol) Potential * 59.244 * 0.9410.97566.35631 (kJ/mol) Total Energy106.647 115.48286.78792 (kJ/mol) *equivalent number of molecules as in liquid* ( large box 20 nm) Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.16367 0.053 0.171542 0.374027 (kJ/mol) Coulomb (SR)11.2894 0.230.49105 -1.44437 (kJ/mol) Potential * 63.2369*1.12.472117.69756 (kJ/mol) Total Energy114.3371.12.655477.72258 (kJ/mol) Since pbc is set to NO molecules leave the box and I dont know if this all right. I hope the difference is acceptable...! For pbc = no there is no box. 0- I am going to do the same calculation but for some polymers solvated in the alkane. For binary system do I need to look at nonboded terms? and then run a simulation for a single polymer in vacuum? Can you please provide me with a recipe for Delta Hvap of the solute in a solvent? The method for calculating heat of vaporization is not dependent upon the contents of the system; it is a fundamental thermodynamic definition. Heat of vaporization is not something that can be calculated from a solute in a solvent. You can calculate DHvap for a particular system, but not some subset of that system. Thanks Justin. I am interested in the energy required to vaporize the solute in a particular solvent not the whole DHvap of the mixture. do you think this can be achieved by calculating nonbonded energies between solute and solvent? ( defining energy groups ..) 1- If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? The PME-related terms contain both solute-solvent, solvent-solvent, and potentially solute-solute terms (depending on the size and nature of the solute), so trying to interpret this term in some pairwise fashion is an exercise in futility. What you mean is when one uses PME interaction energies between components can not be decomposed? So the energy groups I defined to extract nonbonded energies are not giving correct values? Sofar I have been defining energy groups to calculate nonbonded terms between components _A-A A_B... I hope I have not been doing thing wrongly! Please help me out! Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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
Re: [gmx-users] Heat of vap
Elisabeth wrote: Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: To get heat of vaporization, you shouldn't be simulating just a single molecule in the gas phase, it should be an equivalent number of molecules as you have in the liquid phase. Hello David and Justin, My explanation was not clear. Below is the results for liquid phase and for gas phase I tried two cases: one single molecule and the other time for equivalent number of molecules as in liquid phase and thats why results are very similar. ( However Justin says one single molecule is not correct. I think when cutoffs is set to zero only bonded terms are What is not correct is comparing the potential energy of a liquid system of many molecules with a gas phase of a single molecule. Whether or not that was something you did still is not entirely clear, but to be very clear, that's what I was saying is incorrect to do. DHvap is based on conversion of equivalent systems between liquid and gas. treated and even where there are many particles in gas phase to get This is incorrect. Cutoffs of zero mean that all nonbonded interactions are calculated, they are not truncated. energies per mole of molecules i.e g_energy -nmol XXX must be used so values should be colse to a single molecules case.. please correct me! Anyway results for gas phase are close and this is not the issue now). You shouldn't need -nmol for any of this. Simply take the potential energy of the two systems (with equivalent numbers of molecules) and apply the formula I gave you several emails ago. -Justin Liquid phase: Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-27.3083 0.01 0.296591 -0.0389173 (kJ/mol) Coulomb (SR)6.00527 0.0074 0.122878 0.00576827 (kJ/mol) Coul. recip.5.59559 0.0032 0.0557413 0.00316957 (kJ/mol) Potential *34.6779 *0.0251.03468 -0.11177 (kJ/mol) Total Energy86.4044 0.0261.44353 -0.112587 (kJ/mol) *one single molecule in gas phase* Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.24473 0.073 1.292 0.342696 (kJ/mol) Coulomb (SR)11.5723 0.552.17577 -2.33224 (kJ/mol) Potential * 59.244 * 0.9410.9756 6.35631 (kJ/mol) Total Energy106.647 115.4828 6.78792 (kJ/mol) *equivalent number of molecules as in liquid* ( large box 20 nm) Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.16367 0.053 0.171542 0.374027 (kJ/mol) Coulomb (SR)11.2894 0.230.49105 -1.44437 (kJ/mol) Potential * 63.2369*1.12.47211 7.69756 (kJ/mol) Total Energy114.3371.12.65547 7.72258 (kJ/mol) Since pbc is set to NO molecules leave the box and I dont know if this all right. I hope the difference is acceptable...! For pbc = no there is no box. 0- I am going to do the same calculation but for some polymers solvated in the alkane. For binary system do I need to look at nonboded terms? and then run a simulation for a single polymer in vacuum? Can you please provide me with a recipe for Delta Hvap of the solute in a solvent? The method for calculating heat of vaporization is not dependent upon the contents of the system; it is a fundamental thermodynamic definition. Heat of vaporization is not something that can be calculated from a solute in a solvent. You can calculate DHvap for a particular system, but not some subset of that system. Thanks Justin. I am interested in the energy required to vaporize the solute in a particular solvent not the whole DHvap of the mixture. do you think this can be achieved by calculating nonbonded energies between solute and solvent? ( defining energy groups ..) 1- If I want to look at nonboded interactions only,
Re: [gmx-users] Heat of vap
Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: To get heat of vaporization, you shouldn't be simulating just a single molecule in the gas phase, it should be an equivalent number of molecules as you have in the liquid phase. *one single molecule in gas phase* Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.24473 0.073 1.292 0.342696 (kJ/mol) Coulomb (SR)11.5723 0.552.17577 -2.33224 (kJ/mol) Potential * 59.244 * 0.9410.97566.35631 (kJ/mol) Total Energy106.647 115.48286.78792 (kJ/mol) *equivalent number of molecules as in liquid* ( large box 20 nm) Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR)-2.16367 0.053 0.171542 0.374027 (kJ/mol) Coulomb (SR)11.2894 0.230.49105 -1.44437 (kJ/mol) Potential * 63.2369*1.12.472117.69756 (kJ/mol) Total Energy114.3371.12.655477.72258 (kJ/mol) Since pbc is set to NO molecules leave the box and I dont know if this all right. I hope the difference is acceptable...! For pbc = no there is no box. 0- I am going to do the same calculation but for some polymers solvated in the alkane. For binary system do I need to look at nonboded terms? and then run a simulation for a single polymer in vacuum? Can you please provide me with a recipe for Delta Hvap of the solute in a solvent? The method for calculating heat of vaporization is not dependent upon the contents of the system; it is a fundamental thermodynamic definition. Heat of vaporization is not something that can be calculated from a solute in a solvent. You can calculate DHvap for a particular system, but not some subset of that system. 1- If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? The PME-related terms contain both solute-solvent, solvent-solvent, and potentially solute-solute terms (depending on the size and nature of the solute), so trying to interpret this term in some pairwise fashion is an exercise in futility. -Justin coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.0 ff: OPLSAA Appreciate your help, Best, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) 2- How can I compute Ugas? I have liquid now... Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
On 2011-03-31 18.52, Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? Either Epot or Etot. It does not matter if you simulate at the same Temp. You could also consider using the enthalphy (gmx 4.5 and higher). http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) 2- How can I compute Ugas? I have liquid now... Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto: jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? It is delta Hvap/volume. It is directly related to Hvap. What is happening is that they are calculating nonbonded energy of some chains, divide by number of chains and substract from nonbonded energy of a single chain in vacuum. These are the steps I wrote in my first post but I think I should not have included kinetic and should just look at LJ-SR and Coulomb-SR. I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Many thanks... -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
Elisabeth wrote: On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? It is delta Hvap/volume. It is directly related to Hvap. What is happening is that they are calculating nonbonded energy of some chains, divide by number of chains and substract from nonbonded energy of a single chain in vacuum. These are the steps I wrote in my first post but I think I should not have included kinetic and should just look at LJ-SR and Coulomb-SR. I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... PME energies are from nonbonded interactions. The mesh energy is written to the Coul-recip term in the .edr file. If there is some other Coul (LR) term, it is because you're using a twin-range cutoff such that rcoulomb rlist, which I do not believe is correct when using PME. In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Make a box with an equivalent number of molecules separated by some large amount of space (i.e. 50 nm or so). Set pbc=no and all cutoffs to zero. I'm basing this on Gromos96 parameterization, but I don't know what your target force field is. -Justin Many thanks... -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry
Re: [gmx-users] Heat of vap
On 2011-03-31 19.11, Elisabeth wrote: On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? It is delta Hvap/volume. It is directly related to Hvap. What is happening is that they are calculating nonbonded energy of some chains, divide by number of chains and substract from nonbonded energy of a single chain in vacuum. These are the steps I wrote in my first post but I think I should not have included kinetic and should just look at LJ-SR and Coulomb-SR. I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... It is simple. Compute Epot with all normal liquid options (PME, Dispcorr etc.). Compute Epot for a gas phase molecule without any cutoffs Apply equation below. For OPLS/AA we obtain close to 98% correlation between experiment and simulation (paper submitted). In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Many thanks... -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org
Re: [gmx-users] Heat of vap
On 2011-03-30 21.22, Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) do turn off all pbc and cutoff for that one. Thanking you all, Regards, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heat of vap
Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT I have seen this equation used in a number of other studies, as well. -Justin Thanking you all, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
