RE: [gmx-users] CHARMM36 lipid bilayers
Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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] CHARMM36 lipid bilayers
Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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] CHARMM36 lipid bilayers
Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the Supporting Info) using a 1.1 nm cut-off for the switching compared to the 0.8 nm cut-off in their CHARMM simulations. I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM tip3p water. This gives me the closest results in terms of area per lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM results) and experiment. Cheers Tom Sven Jakobtorweihen wrote: Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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 -- Dr Thomas Piggot University of Southampton, UK. -- 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
Re: [gmx-users] CHARMM36 lipid bilayers
I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the Supporting Info) using a 1.1 nm cut-off for the switching compared to the 0.8 nm cut-off in their CHARMM simulations. I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM tip3p water. This gives me the closest results in terms of area per lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM results) and experiment. Cheers Tom Sven Jakobtorweihen wrote: Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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 -- Dr Thomas Piggot University of Southampton, UK. Pär Bjelkmar, Ph.D. student Stockholm Center for Biomembrane
Re: [gmx-users] CHARMM36 lipid bilayers
Yes, I was surprised as well. It depends on the value of rvdw-switch. For some systems it can be 10 A^2, for others much smaller. Tom Pär Bjelkmar wrote: I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the Supporting Info) using a 1.1 nm cut-off for the switching compared to the 0.8 nm cut-off in their CHARMM simulations. I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM tip3p water. This gives me the closest results in terms of area per lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM results) and experiment. Cheers Tom Sven Jakobtorweihen wrote: Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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
Re: [gmx-users] CHARMM36 lipid bilayers
Hi there, Tom, many thanks for your valuable suggestions. I am also surprised by this large influence. For DPPC the change is about 5 A^2 (same settings but different water model). Cheers, Sven Pär Bjelkmar schrieb: I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the Supporting Info) using a 1.1 nm cut-off for the switching compared to the 0.8 nm cut-off in their CHARMM simulations. I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM tip3p water. This gives me the closest results in terms of area per lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM results) and experiment. Cheers Tom Sven Jakobtorweihen wrote: Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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
RE: [gmx-users] CHARMM36 lipid bilayers
Hi, You have very strange and complex cut-off settings in Gromacs. What Charmm settings are you trying to mimic? Berk Date: Thu, 21 Oct 2010 15:03:51 +0200 From: jakobtorwei...@tuhh.de To: gmx-users@gromacs.org Subject: [gmx-users] CHARMM36 lipid bilayers Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- 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] CHARMM36 lipid bilayers
Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- 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
