Re: [gmx-users] confusion on NPT MD simulation
On 6/18/15 6:28 AM, Ming Tang wrote: Dear Tsjerk and Justin, Thanks for your help. I have tried to use 1000 and 1 to restrained the whole protein during NPT equilibration, but found the protein shape changed as well. Is position restraint compatible with pressure coupling? Restraints are compatible with pressure coupling. Too high of a restraint can generate spurious forces, as Tsjerk mentioned below. Note that restraints are just biasing potentials; they can allow for small changes in the structure. You shouldn't necessarily hike the force constant to some high value to try to absolutely fix the atoms. -Justin Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 17 June 2015 1:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] confusion on NPT MD simulation Hi Ming Tang, You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well. Cheers, Tsjerk On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thank you so much. There are another 2 papers in which the authors said they equilibrated their collagen like this. This really made me confused for quite a long time, and I come to you for help finally. Critical analysis is important. In the steps to perform a simulation page, step 8 indicates that NPT equilibration is for fixing the density. I have been confused about how should I equilibrate my collagen before SMD simulation. I want to keep the shape (do not change its length) of my collagen during equilibration, so that the force-deformation curve will not be changed because of the equilibration process. After knowing that freezing and pressure coupling is incompatible, I tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the simulation to SMD (actually umbrella and direction-periodic are used) directly in NVT. The simulation run smoothly and I got my force-deformation curve, but I am still concerned whether my equilibration is good enough for SMD simulation, and whether the results are credible. If I choose to further equilibrate my collagen in NPT after in NVT, is it feasible to restrain parts (backbone, terminal atoms) of my collagen by adding a huge force constant (say 1*10e6 kJ/mol/nm^2) through -fc in genrestr command, so that its shape will be reserved during the equilibration? Could you please kindly give me some guidance on which is the best equilibration process I show follow to get a good starting point for SMD (umbrella+direction-periodic) simulation? Thank you so much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 16 June 2015 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? People are often lazy (or inconsistent) with language. Holding something fixed might mean huge restraint or it might actually mean frozen (freezegrps in the .mdp). There are functional differences between these two. Atoms are also not constrained (that's a restraint!) in GROMACS, so there may be some loose language here... If you have questions about methods for published work relevant to what you're doing, that's what corresponding authors are for! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
Re: [gmx-users] confusion on NPT MD simulation
Dear Justin, I tried to equilibrate my collagen with all the heavy atoms restrained using define = -DPOSRES in NPT for 300 ps, but found that the collagen became much shorter. The restrained force for the heavy atoms generated through pdb2gmx is 1000 kJ/mol/nm by default, why does the length changed a lot? Thank you. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 18 June 2015 9:34 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/18/15 6:28 AM, Ming Tang wrote: Dear Tsjerk and Justin, Thanks for your help. I have tried to use 1000 and 1 to restrained the whole protein during NPT equilibration, but found the protein shape changed as well. Is position restraint compatible with pressure coupling? Restraints are compatible with pressure coupling. Too high of a restraint can generate spurious forces, as Tsjerk mentioned below. Note that restraints are just biasing potentials; they can allow for small changes in the structure. You shouldn't necessarily hike the force constant to some high value to try to absolutely fix the atoms. -Justin Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 17 June 2015 1:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] confusion on NPT MD simulation Hi Ming Tang, You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well. Cheers, Tsjerk On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thank you so much. There are another 2 papers in which the authors said they equilibrated their collagen like this. This really made me confused for quite a long time, and I come to you for help finally. Critical analysis is important. In the steps to perform a simulation page, step 8 indicates that NPT equilibration is for fixing the density. I have been confused about how should I equilibrate my collagen before SMD simulation. I want to keep the shape (do not change its length) of my collagen during equilibration, so that the force-deformation curve will not be changed because of the equilibration process. After knowing that freezing and pressure coupling is incompatible, I tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the simulation to SMD (actually umbrella and direction-periodic are used) directly in NVT. The simulation run smoothly and I got my force-deformation curve, but I am still concerned whether my equilibration is good enough for SMD simulation, and whether the results are credible. If I choose to further equilibrate my collagen in NPT after in NVT, is it feasible to restrain parts (backbone, terminal atoms) of my collagen by adding a huge force constant (say 1*10e6 kJ/mol/nm^2) through -fc in genrestr command, so that its shape will be reserved during the equilibration? Could you please kindly give me some guidance on which is the best equilibration process I show follow to get a good starting point for SMD (umbrella+direction-periodic) simulation? Thank you so much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 16 June 2015 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? People are often lazy (or inconsistent) with language. Holding something fixed might mean huge restraint or it might actually mean frozen (freezegrps
Re: [gmx-users] confusion on NPT MD simulation
Dear Justin, I tried again, and the position restraint works well in NPT equilibration. Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang Sent: Friday, 19 June 2015 11:08 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation Dear Justin, I tried to equilibrate my collagen with all the heavy atoms restrained using define = -DPOSRES in NPT for 300 ps, but found that the collagen became much shorter. The restrained force for the heavy atoms generated through pdb2gmx is 1000 kJ/mol/nm by default, why does the length changed a lot? Thank you. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 18 June 2015 9:34 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/18/15 6:28 AM, Ming Tang wrote: Dear Tsjerk and Justin, Thanks for your help. I have tried to use 1000 and 1 to restrained the whole protein during NPT equilibration, but found the protein shape changed as well. Is position restraint compatible with pressure coupling? Restraints are compatible with pressure coupling. Too high of a restraint can generate spurious forces, as Tsjerk mentioned below. Note that restraints are just biasing potentials; they can allow for small changes in the structure. You shouldn't necessarily hike the force constant to some high value to try to absolutely fix the atoms. -Justin Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 17 June 2015 1:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] confusion on NPT MD simulation Hi Ming Tang, You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well. Cheers, Tsjerk On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thank you so much. There are another 2 papers in which the authors said they equilibrated their collagen like this. This really made me confused for quite a long time, and I come to you for help finally. Critical analysis is important. In the steps to perform a simulation page, step 8 indicates that NPT equilibration is for fixing the density. I have been confused about how should I equilibrate my collagen before SMD simulation. I want to keep the shape (do not change its length) of my collagen during equilibration, so that the force-deformation curve will not be changed because of the equilibration process. After knowing that freezing and pressure coupling is incompatible, I tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the simulation to SMD (actually umbrella and direction-periodic are used) directly in NVT. The simulation run smoothly and I got my force-deformation curve, but I am still concerned whether my equilibration is good enough for SMD simulation, and whether the results are credible. If I choose to further equilibrate my collagen in NPT after in NVT, is it feasible to restrain parts (backbone, terminal atoms) of my collagen by adding a huge force constant (say 1*10e6 kJ/mol/nm^2) through -fc in genrestr command, so that its shape will be reserved during the equilibration? Could you please kindly give me some guidance on which is the best equilibration process I show follow to get a good starting point for SMD (umbrella+direction-periodic) simulation? Thank you so much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 16 June 2015 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms
Re: [gmx-users] confusion on NPT MD simulation
Dear Tsjerk and Justin, Thanks for your help. I have tried to use 1000 and 1 to restrained the whole protein during NPT equilibration, but found the protein shape changed as well. Is position restraint compatible with pressure coupling? Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 17 June 2015 1:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] confusion on NPT MD simulation Hi Ming Tang, You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well. Cheers, Tsjerk On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thank you so much. There are another 2 papers in which the authors said they equilibrated their collagen like this. This really made me confused for quite a long time, and I come to you for help finally. Critical analysis is important. In the steps to perform a simulation page, step 8 indicates that NPT equilibration is for fixing the density. I have been confused about how should I equilibrate my collagen before SMD simulation. I want to keep the shape (do not change its length) of my collagen during equilibration, so that the force-deformation curve will not be changed because of the equilibration process. After knowing that freezing and pressure coupling is incompatible, I tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the simulation to SMD (actually umbrella and direction-periodic are used) directly in NVT. The simulation run smoothly and I got my force-deformation curve, but I am still concerned whether my equilibration is good enough for SMD simulation, and whether the results are credible. If I choose to further equilibrate my collagen in NPT after in NVT, is it feasible to restrain parts (backbone, terminal atoms) of my collagen by adding a huge force constant (say 1*10e6 kJ/mol/nm^2) through -fc in genrestr command, so that its shape will be reserved during the equilibration? Could you please kindly give me some guidance on which is the best equilibration process I show follow to get a good starting point for SMD (umbrella+direction-periodic) simulation? Thank you so much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 16 June 2015 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? People are often lazy (or inconsistent) with language. Holding something fixed might mean huge restraint or it might actually mean frozen (freezegrps in the .mdp). There are functional differences between these two. Atoms are also not constrained (that's a restraint!) in GROMACS, so there may be some loose language here... If you have questions about methods for published work relevant to what you're doing, that's what corresponding authors are for! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests
Re: [gmx-users] confusion on NPT MD simulation
Hi Ming Tang, You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well. Cheers, Tsjerk On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thank you so much. There are another 2 papers in which the authors said they equilibrated their collagen like this. This really made me confused for quite a long time, and I come to you for help finally. Critical analysis is important. In the steps to perform a simulation page, step 8 indicates that NPT equilibration is for fixing the density. I have been confused about how should I equilibrate my collagen before SMD simulation. I want to keep the shape (do not change its length) of my collagen during equilibration, so that the force-deformation curve will not be changed because of the equilibration process. After knowing that freezing and pressure coupling is incompatible, I tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the simulation to SMD (actually umbrella and direction-periodic are used) directly in NVT. The simulation run smoothly and I got my force-deformation curve, but I am still concerned whether my equilibration is good enough for SMD simulation, and whether the results are credible. If I choose to further equilibrate my collagen in NPT after in NVT, is it feasible to restrain parts (backbone, terminal atoms) of my collagen by adding a huge force constant (say 1*10e6 kJ/mol/nm^2) through -fc in genrestr command, so that its shape will be reserved during the equilibration? Could you please kindly give me some guidance on which is the best equilibration process I show follow to get a good starting point for SMD (umbrella+direction-periodic) simulation? Thank you so much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 16 June 2015 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? People are often lazy (or inconsistent) with language. Holding something fixed might mean huge restraint or it might actually mean frozen (freezegrps in the .mdp). There are functional differences between these two. Atoms are also not constrained (that's a restraint!) in GROMACS, so there may be some loose language here... If you have questions about methods for published work relevant to what you're doing, that's what corresponding authors are for! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
Re: [gmx-users] confusion on NPT MD simulation
Dear Justin, Thank you so much. There are another 2 papers in which the authors said they equilibrated their collagen like this. This really made me confused for quite a long time, and I come to you for help finally. Critical analysis is important. In the steps to perform a simulation page, step 8 indicates that NPT equilibration is for fixing the density. I have been confused about how should I equilibrate my collagen before SMD simulation. I want to keep the shape (do not change its length) of my collagen during equilibration, so that the force-deformation curve will not be changed because of the equilibration process. After knowing that freezing and pressure coupling is incompatible, I tried to use NVT with heavy atoms restrained by using -DPOSRES, and further the simulation to SMD (actually umbrella and direction-periodic are used) directly in NVT. The simulation run smoothly and I got my force-deformation curve, but I am still concerned whether my equilibration is good enough for SMD simulation, and whether the results are credible. If I choose to further equilibrate my collagen in NPT after in NVT, is it feasible to restrain parts (backbone, terminal atoms) of my collagen by adding a huge force constant (say 1*10e6 kJ/mol/nm^2) through -fc in genrestr command, so that its shape will be reserved during the equilibration? Could you please kindly give me some guidance on which is the best equilibration process I show follow to get a good starting point for SMD (umbrella+direction-periodic) simulation? Thank you so much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 16 June 2015 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? People are often lazy (or inconsistent) with language. Holding something fixed might mean huge restraint or it might actually mean frozen (freezegrps in the .mdp). There are functional differences between these two. Atoms are also not constrained (that's a restraint!) in GROMACS, so there may be some loose language here... If you have questions about methods for published work relevant to what you're doing, that's what corresponding authors are for! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] confusion on NPT MD simulation
Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? Thanks in advance. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang Sent: Monday, 15 June 2015 6:05 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them? As you mentioned, freezing and pressure coupling are incompatible. My first understanding was that I cannot fix atoms during NPT. Therefore, I have been steering my collagen in NVT recently. After minimization, I equilibrated my collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, and then stretched it using pull code. Do you think this simple process can give a good starting point for SMD? Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.semailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 1 June 2015 9:46 PM To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/1/15 4:40 AM, Ming Tang wrote: Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout= 1 xtc-precision= 10 cutoff-scheme= verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t= 1.0 1.0 ref-t= 310 310 Pcoupl = parrinello-Rahman Pcoupltype = isotropic tau-p= 5 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz freezegrps = C freezedim= Y Y Y C is a group containing atoms of both the first and the last residues in all the three chains. But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation? Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed. I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate. Freezing and pressure coupling are incompatible; see notes in the manual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edumailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] confusion on NPT MD simulation
On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained. I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? People are often lazy (or inconsistent) with language. Holding something fixed might mean huge restraint or it might actually mean frozen (freezegrps in the .mdp). There are functional differences between these two. Atoms are also not constrained (that's a restraint!) in GROMACS, so there may be some loose language here... If you have questions about methods for published work relevant to what you're doing, that's what corresponding authors are for! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] confusion on NPT MD simulation
If your protein structure is retained, your procedure is all right. On Mon, Jun 15, 2015 at 5:04 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them? As you mentioned, freezing and pressure coupling are incompatible. My first understanding was that I cannot fix atoms during NPT. Therefore, I have been steering my collagen in NVT recently. After minimization, I equilibrated my collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, and then stretched it using pull code. Do you think this simple process can give a good starting point for SMD? Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 1 June 2015 9:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/1/15 4:40 AM, Ming Tang wrote: Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout= 1 xtc-precision= 10 cutoff-scheme= verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t= 1.0 1.0 ref-t= 310 310 Pcoupl = parrinello-Rahman Pcoupltype = isotropic tau-p= 5 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz freezegrps = C freezedim= Y Y Y C is a group containing atoms of both the first and the last residues in all the three chains. But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation? Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed. I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate. Freezing and pressure coupling are incompatible; see notes in the manual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] confusion on NPT MD simulation
Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them? As you mentioned, freezing and pressure coupling are incompatible. My first understanding was that I cannot fix atoms during NPT. Therefore, I have been steering my collagen in NVT recently. After minimization, I equilibrated my collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, and then stretched it using pull code. Do you think this simple process can give a good starting point for SMD? Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 1 June 2015 9:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/1/15 4:40 AM, Ming Tang wrote: Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout= 1 xtc-precision= 10 cutoff-scheme= verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t= 1.0 1.0 ref-t= 310 310 Pcoupl = parrinello-Rahman Pcoupltype = isotropic tau-p= 5 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz freezegrps = C freezedim= Y Y Y C is a group containing atoms of both the first and the last residues in all the three chains. But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation? Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed. I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate. Freezing and pressure coupling are incompatible; see notes in the manual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] confusion on NPT MD simulation
On 6/1/15 4:40 AM, Ming Tang wrote: Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout= 1 xtc-precision= 10 cutoff-scheme= verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t= 1.0 1.0 ref-t= 310 310 Pcoupl = parrinello-Rahman Pcoupltype = isotropic tau-p= 5 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz freezegrps = C freezedim= Y Y Y C is a group containing atoms of both the first and the last residues in all the three chains. But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation? Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed. I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate. Freezing and pressure coupling are incompatible; see notes in the manual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
