Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Sorry. I simulate DOPG not POPG. Thank you anyway. On Dec 13, 2007 6:53 PM, Alan Dodd [EMAIL PROTECTED] wrote: What topology are you using? If you're using one based on the Kartunnen's group POPG (the only publicly available one I know of), then be aware that I think they saw gel phase too. Oh, and read the email you replied to, particularly the bit about 18 angstroms. - Original Message From: Myunggi Yi [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 13, 2007 6:48:20 PM Subject: Re: [gmx-users] Gel Phase in DMPC using Berger force field ?? I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi [EMAIL PROTECTED] wrote: Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi [EMAIL PROTECTED] wrote: Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] . Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
What topology are you using? If you're using one based on the Kartunnen's group POPG (the only publicly available one I know of), then be aware that I think they saw gel phase too. Oh, and read the email you replied to, particularly the bit about 18 angstroms. - Original Message From: Myunggi Yi [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 13, 2007 6:48:20 PM Subject: Re: [gmx-users] Gel Phase in DMPC using Berger force field ?? I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi [EMAIL PROTECTED] wrote: Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Yes, this should be attempted. Perhaps the ultimate test of a force field is to nail a phase change. At 03:34 AM 12/12/2007, you wrote: Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Dear all, For the gel-to-liquid crystalline phase transition in DPPC and DPPE there is a paper: Leekumjorn and Sum, BBA, 1768 (2007) 354-365 I've found it several month ago and I haven't red through it completely, but they used the Berger force field. Best, Zoltan Eric Jakobsson [EMAIL PROTECTED] wrote: Yes, this should be attempted. Perhaps the ultimate test of a force field is to nail a phase change. At 03:34 AM 12/12/2007, you wrote: Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
