Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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] Surface tension readings in NVT vs NPT simulations
David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se http://folding.bmc.uu.se -- gmx-users mailing list 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. 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] Surface tension readings in NVT vs NPT simulations
I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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 -- 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] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 16.59, Denny Frost wrote: Is that using anisotropic pressure coupling? yes. just try it On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 17.28, Denny Frost wrote: No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work. On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
It won't take zero with the berendsen thermostat, but I only wish to do weak coupling for now. Yes, I only specified the two values for semiisotropic. What I'm asking is will this setup only do z-pressure coupling? On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 17.28, Denny Frost wrote: No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work. On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as
