Re: [gmx-users] Protein-POPC bilayer
Dear Dr.Dallas, Would you mind please sending the article as soon as it's printed? I would appreciate you. Thanks. Regards, Shima From: Dallas Warren dallas.war...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 17, 2012 7:30 AM Subject: RE: [gmx-users] Protein-POPC bilayer Not directly related to bilayers, but our work with liquid phases has found some interesting things with anisotropic versus isotropic. Basically, even though anisotropic allows things to structure without constraints to how they want to be, there is some artifacts that drive it too far, beyond what is reasonable and you get severe box distortion and failure. Will be saying a little on that in an upcoming paper Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: Friday, 17 August 2012 12:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Protein-POPC bilayer On 8/16/12 10:21 PM, Mark Abraham wrote: On 17/08/2012 11:46 AM, Justin Lemkul wrote: On 8/16/12 9:43 PM, Jianguo Li wrote: What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. What I generally see is basically the opposite. Using anisotropic pressure coupling leads to a steady change in box dimensions, but this is not the case with semiisotropic coupling. It depends, I suppose, on how one produces the membrane protein system - adequate deletion of lipids can accommodate for a protein of any shape without affecting box vectors. Or depends on the force field or lipid? Certainly a possibility. I think that the statement in the manual makes it pretty clear though that the algorithm itself is likely responsible for at least some of the observed deformations - Beware that anisotropic scaling can lead to extreme deformation of the simulation box. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Protein-POPC bilayer
After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method. --Jianguo From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 17 August 2012, 7:26 Subject: [gmx-users] Protein-POPC bilayer Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Protein-POPC bilayer
On 8/16/12 9:14 PM, Jianguo Li wrote: After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method. Most pre-equilibrated bilayers have (roughly) equivalent x and y box dimensions. Why do you think they should inherently be different? In my experience, anisotropic coupling leads to major deformations in the x-y plane, taking a bilayer that is initially a square (roughly) in the x-y plane and turning it into a rectangle. I'd be very curious to hear Peter's answer to this question. I used to use anisotropic coupling, but now I use semiisotropic exclusively. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. --Jianguo From: Justin Lemkul jalem...@vt.edu To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 17 August 2012, 9:19 Subject: Re: [gmx-users] Protein-POPC bilayer On 8/16/12 9:14 PM, Jianguo Li wrote: After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method. Most pre-equilibrated bilayers have (roughly) equivalent x and y box dimensions. Why do you think they should inherently be different? In my experience, anisotropic coupling leads to major deformations in the x-y plane, taking a bilayer that is initially a square (roughly) in the x-y plane and turning it into a rectangle. I'd be very curious to hear Peter's answer to this question. I used to use anisotropic coupling, but now I use semiisotropic exclusively. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
On 8/16/12 9:43 PM, Jianguo Li wrote: What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. What I generally see is basically the opposite. Using anisotropic pressure coupling leads to a steady change in box dimensions, but this is not the case with semiisotropic coupling. It depends, I suppose, on how one produces the membrane protein system - adequate deletion of lipids can accommodate for a protein of any shape without affecting box vectors. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
On 17/08/2012 11:46 AM, Justin Lemkul wrote: On 8/16/12 9:43 PM, Jianguo Li wrote: What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. What I generally see is basically the opposite. Using anisotropic pressure coupling leads to a steady change in box dimensions, but this is not the case with semiisotropic coupling. It depends, I suppose, on how one produces the membrane protein system - adequate deletion of lipids can accommodate for a protein of any shape without affecting box vectors. Or depends on the force field or lipid? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
You always use semi-isotropic for bilayer work. The Z is decoupled from x-y due to symmetry. I don't think I mention anything differently in the paper. Pcoupltype = semiisotropic On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote: Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
On 8/16/12 10:21 PM, Mark Abraham wrote: On 17/08/2012 11:46 AM, Justin Lemkul wrote: On 8/16/12 9:43 PM, Jianguo Li wrote: What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. What I generally see is basically the opposite. Using anisotropic pressure coupling leads to a steady change in box dimensions, but this is not the case with semiisotropic coupling. It depends, I suppose, on how one produces the membrane protein system - adequate deletion of lipids can accommodate for a protein of any shape without affecting box vectors. Or depends on the force field or lipid? Certainly a possibility. I think that the statement in the manual makes it pretty clear though that the algorithm itself is likely responsible for at least some of the observed deformations - Beware that anisotropic scaling can lead to extreme deformation of the simulation box. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md; leap-frog integrator nsteps = 250 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation= yes; NOT first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= no; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp= 300 ; temperature for Maxwell distribution ;gen_seed= -1; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = POPC SOL On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote: You always use semi-isotropic for bilayer work. The Z is decoupled from x-y due to symmetry. I don't think I mention anything differently in the paper. Pcoupltype = semiisotropic On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote: Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-POPC bilayer
Not directly related to bilayers, but our work with liquid phases has found some interesting things with anisotropic versus isotropic. Basically, even though anisotropic allows things to structure without constraints to how they want to be, there is some artifacts that drive it too far, beyond what is reasonable and you get severe box distortion and failure. Will be saying a little on that in an upcoming paper Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: Friday, 17 August 2012 12:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Protein-POPC bilayer On 8/16/12 10:21 PM, Mark Abraham wrote: On 17/08/2012 11:46 AM, Justin Lemkul wrote: On 8/16/12 9:43 PM, Jianguo Li wrote: What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. What I generally see is basically the opposite. Using anisotropic pressure coupling leads to a steady change in box dimensions, but this is not the case with semiisotropic coupling. It depends, I suppose, on how one produces the membrane protein system - adequate deletion of lipids can accommodate for a protein of any shape without affecting box vectors. Or depends on the force field or lipid? Certainly a possibility. I think that the statement in the manual makes it pretty clear though that the algorithm itself is likely responsible for at least some of the observed deformations - Beware that anisotropic scaling can lead to extreme deformation of the simulation box. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Protein-POPC bilayer
In 2.1.6. Membrane bilayer construction part of the article you mentioned: Asingle POPC molecule is parameterized using a CHARMM36 force field conversion for GROMACS7. The result- ing system,which consists of around 238 lipids is then equilibrated for at least 50 ns at 310 K and 1 atm under NPT ensemble with anisotropic pressure coupling or until the are a per lipid converges close to the consensus value of around 63–65Å per headgroup. This is where I asked the question about. Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 17, 2012 7:17 AM Subject: Re: [gmx-users] Protein-POPC bilayer Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md ; leap-frog integrator nsteps = 250 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes ; NOT first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 300 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = POPC SOL On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote: You always use semi-isotropic for bilayer work. The Z is decoupled from x-y due to symmetry. I don't think I mention anything differently in the paper. Pcoupltype = semiisotropic On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote: Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- == Peter C. Lai | University of Alabama-Birmingham
Re: [gmx-users] Protein-POPC bilayer
Can't remember why I said that, since it's not what I used. Stupid autocorrect? Sorry! On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote: In 2.1.6. Membrane bilayer construction part of the article you mentioned: Asingle POPC molecule is parameterized using a CHARMM36 force field conversion for GROMACS7. The result- ing system,which consists of around 238 lipids is then equilibrated for at least 50 ns at 310 K and 1 atm under NPT ensemble with anisotropic pressure coupling or until the are a per lipid converges close to the consensus value of around 63–65Å per headgroup. This is where I asked the question about. Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 17, 2012 7:17 AM Subject: Re: [gmx-users] Protein-POPC bilayer Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md ; leap-frog integrator nsteps = 250 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes ; NOT first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 300 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = POPC SOL On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote: You always use semi-isotropic for bilayer work. The Z is decoupled from x-y due to symmetry. I don't think I mention anything differently in the paper. Pcoupltype = semiisotropic On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote: Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] Protein-POPC bilayer
Oh, It's OK. Thanks Peter. :-) I used the the same .mdp file sent me by you 1 month ago, for the pre-equilibration of POPC in water. But as others said here, anisotropic pressure coupling might result in major changes in lipid bilayer. I don't know, but it seems it is better to use anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! Anisotropic would be a better option? Now, I'd like to know which one is suggested to be used for the pre-equilibration before insertion of protein? Anisotropic is suggested? Please make me clear here. Thanks for all explanations. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 17, 2012 8:19 AM Subject: Re: [gmx-users] Protein-POPC bilayer Can't remember why I said that, since it's not what I used. Stupid autocorrect? Sorry! On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote: In 2.1.6. Membrane bilayer construction part of the article you mentioned: Asingle POPC molecule is parameterized using a CHARMM36 force field conversion for GROMACS7. The result- ing system,which consists of around 238 lipids is then equilibrated for at least 50 ns at 310 K and 1 atm under NPT ensemble with anisotropic pressure coupling or until the are a per lipid converges close to the consensus value of around 63–65Å per headgroup. This is where I asked the question about. Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 17, 2012 7:17 AM Subject: Re: [gmx-users] Protein-POPC bilayer Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md ; leap-frog integrator nsteps = 250 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes ; NOT first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 300 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = POPC SOL On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote: You always use semi-isotropic for bilayer work. The Z is decoupled from x-y due to symmetry. I don't think I mention anything differently in the paper. Pcoupltype = semiisotropic On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote: Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might
Re: [gmx-users] Protein-POPC bilayer
On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote: Oh, It's OK. Thanks Peter. :-) I used the the same .mdp file sent me by you 1 month ago, for the pre-equilibration of POPC in water. Well if that worked out, then what is the problem? What do you mean by pre-equlibration The only step that happens before equilibraiton is energy minimzation... If NPT is crashing after EM then try a few ns of NVT (with a V-rescale thermostat) first, but because VMD gives you highly ordered bilayer (straight chains), I believe I was able to go from EM directly to NPT without any problems. But as others said here, anisotropic pressure coupling might result in major changes in lipid bilayer. I don't know, but it seems it is better to use anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! Anisotropic would be a better option? Now, I'd like to know which one is suggested to be used for the pre-equilibration before insertion of protein? Anisotropic is suggested? Please make me clear here. Thanks for all explanations. You are welcome to try using anisotropic pressure coupling. With a system of the size I put forth, it could be large enough[1] to buffer against box shearing forces. [1] Anezo et. al J. Phys. Chem. B 2003, 107, 9424-9433 If you already equilibrated the membrane before insertion then go ahead and do the insertion. As was stated before, if the box vectors and area per lipid are in equilibrium by the end of the equilibration, you should be fine. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 17, 2012 8:19 AM Subject: Re: [gmx-users] Protein-POPC bilayer Can't remember why I said that, since it's not what I used. Stupid autocorrect? Sorry! On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote: In 2.1.6. Membrane bilayer construction part of the article you mentioned: Asingle POPC molecule is parameterized using a CHARMM36 force field conversion for GROMACS7. The result- ing system,which consists of around 238 lipids is then equilibrated for at least 50 ns at 310 K and 1 atm under NPT ensemble with anisotropic pressure coupling or until the are a per lipid converges close to the consensus value of around 63–65Å per headgroup. This is where I asked the question about. Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 17, 2012 7:17 AM Subject: Re: [gmx-users] Protein-POPC bilayer Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md ; leap-frog integrator nsteps = 250 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes ; NOT first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325
Re: [gmx-users] Protein-POPC bilayer
:-) Thanks Peter. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 17, 2012 8:48 AM Subject: Re: [gmx-users] Protein-POPC bilayer On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote: Oh, It's OK. Thanks Peter. :-) I used the the same .mdp file sent me by you 1 month ago, for the pre-equilibration of POPC in water. Well if that worked out, then what is the problem? What do you mean by pre-equlibration The only step that happens before equilibraiton is energy minimzation... If NPT is crashing after EM then try a few ns of NVT (with a V-rescale thermostat) first, but because VMD gives you highly ordered bilayer (straight chains), I believe I was able to go from EM directly to NPT without any problems. But as others said here, anisotropic pressure coupling might result in major changes in lipid bilayer. I don't know, but it seems it is better to use anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! Anisotropic would be a better option? Now, I'd like to know which one is suggested to be used for the pre-equilibration before insertion of protein? Anisotropic is suggested? Please make me clear here. Thanks for all explanations. You are welcome to try using anisotropic pressure coupling. With a system of the size I put forth, it could be large enough[1] to buffer against box shearing forces. [1] Anezo et. al J. Phys. Chem. B 2003, 107, 9424-9433 If you already equilibrated the membrane before insertion then go ahead and do the insertion. As was stated before, if the box vectors and area per lipid are in equilibrium by the end of the equilibration, you should be fine. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 17, 2012 8:19 AM Subject: Re: [gmx-users] Protein-POPC bilayer Can't remember why I said that, since it's not what I used. Stupid autocorrect? Sorry! On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote: In 2.1.6. Membrane bilayer construction part of the article you mentioned: Asingle POPC molecule is parameterized using a CHARMM36 force field conversion for GROMACS7. The result- ing system,which consists of around 238 lipids is then equilibrated for at least 50 ns at 310 K and 1 atm under NPT ensemble with anisotropic pressure coupling or until the are a per lipid converges close to the consensus value of around 63–65Å per headgroup. This is where I asked the question about. Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 17, 2012 7:17 AM Subject: Re: [gmx-users] Protein-POPC bilayer Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md ; leap-frog integrator nsteps = 250 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes ; NOT first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5
