Re: [gmx-users] How to make a lipid bilayer with specific dimensions?
NG HUI WEN wrote: Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman’s website 2) Use genconf –f popc128a.pdb –o popcx2.pdb –nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm) My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I Too big? If you're using either of the two coordinate files above (popc128a.pdb, popcx2.pdb), they should be too small. would like to “crop” the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before. Do I have to use other software to achieve this? If so, I’d really appreciate some pointers. You can do this in three steps. If your goal is to have a single lipid bilayer in the middle of the box, with water around it: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14 genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb The reason you need three steps is that if you supply a z-dimension of 14 in the first genbox command, at least two full bilayers (or some fraction close to it) will be placed in your box. If that's your goal, then this can be done in one step. -Justin Thanks! Email has been scanned for viruses by UNMC email management service http://www.nottingham.edu.my -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] How to make a lipid bilayer with specific dimensions?
I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC). Therefore: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 will give you a bilayer that gets solvated with a water defect around the edges of the initial unit cell and that, after 10 - 200 ns of simulation, gives you an equilibrated bilayer (without water defect) that is much smaller than x=9.6, y=9.5. To get what you want, you need to either start your bilayer with larger x and y (calculate area per lipid in 9.6*9.5 to figure out how many lipids you should have and keep running genbox until you get that), or perhaps a run through inflategro might do it. Chris. --original message -- [gmx-users] How to make a lipid bilayer with specific dimensions? Justin A. Lemkul jalemkul at vt.edu Mon Sep 27 13:00:32 CEST 2010 * Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] NG HUI WEN wrote: Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman?s website 2) Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm) My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I Too big? If you're using either of the two coordinate files above (popc128a.pdb, popcx2.pdb), they should be too small. would like to ?crop? the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before. Do I have to use other software to achieve this? If so, I?d really appreciate some pointers. You can do this in three steps. If your goal is to have a single lipid bilayer in the middle of the box, with water around it: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14 genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb The reason you need three steps is that if you supply a z-dimension of 14 in the first genbox command, at least two full bilayers (or some fraction close to it) will be placed in your box. If that's your goal, then this can be done in one step. -Justin Thanks! Email has been scanned for viruses by UNMC email management service http://www.nottingham.edu.my -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin * Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the gmx-users mailing list -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] How to make a lipid bilayer with specific dimensions?
Thanks for that guys! I will try them out. Just a quick question here with regards to my lipids being possibly too small, does it have something to do with the minimum image criterion for PBC? I have ensured that the distance of edge of the box and the atoms at the side of the protein to be greater than the cutoff of 1.2nm (PME is used)... in the hope that the protein would not interact with it's neighbouring image. I hope I'm not going down the wrong direction in my understanding of pbc... Thanks!!! -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca Sent: Monday, September 27, 2010 8:30 PM To: gmx-users@gromacs.org Subject: [gmx-users] How to make a lipid bilayer with specific dimensions? I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC). Therefore: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 will give you a bilayer that gets solvated with a water defect around the edges of the initial unit cell and that, after 10 - 200 ns of simulation, gives you an equilibrated bilayer (without water defect) that is much smaller than x=9.6, y=9.5. To get what you want, you need to either start your bilayer with larger x and y (calculate area per lipid in 9.6*9.5 to figure out how many lipids you should have and keep running genbox until you get that), or perhaps a run through inflategro might do it. Chris. --original message -- [gmx-users] How to make a lipid bilayer with specific dimensions? Justin A. Lemkul jalemkul at vt.edu Mon Sep 27 13:00:32 CEST 2010 * Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] NG HUI WEN wrote: Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman?s website 2) Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm) My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I Too big? If you're using either of the two coordinate files above (popc128a.pdb, popcx2.pdb), they should be too small. would like to ?crop? the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before. Do I have to use other software to achieve this? If so, I?d really appreciate some pointers. You can do this in three steps. If your goal is to have a single lipid bilayer in the middle of the box, with water around it: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14 genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb The reason you need three steps is that if you supply a z-dimension of 14 in the first genbox command, at least two full bilayers (or some fraction close to it) will be placed in your box. If that's your goal, then this can be done in one step. -Justin Thanks! Email has been scanned for viruses by UNMC email management service http://www.nottingham.edu.my -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin * Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the gmx-users mailing list -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Email has been scanned for viruses by UNMC email management service Email has been scanned for viruses by UNMC email management service -- gmx-users mailing list
Re: [gmx-users] How to make a lipid bilayer with specific dimensions?
NG HUI WEN wrote: Thanks for that guys! I will try them out. Just a quick question here with regards to my lipids being possibly too small, does it have something to do with the minimum image criterion for PBC? I have ensured that the distance of edge of the box and the atoms at the side of the protein to be greater than the cutoff of 1.2nm (PME is used)... in the hope that the protein would not interact with it's neighbouring image. I hope I'm not going down the wrong direction in my understanding of pbc... Thanks!!! There is no direct relationship between genbox and the minimum image convention. You certainly need to build a system that is of sufficient size to avoid spurious PBC interactions, but when genbox does is independent of this fact. The problem is that genbox will not place a molecule that falls partially outside the box, thus deleting an entire lipid and leaving a gap at the edge of the box. Like Chris said, this can lead to your system compressing somewhat to give dimensions smaller than what you were hoping for. Whether or not this is a problem in the long run is up to you to decide based on the specifics of your system. Short answer: make your box slightly larger than you think you need and equilibrate for a long time to ensure that your box is stable. -Justin -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca Sent: Monday, September 27, 2010 8:30 PM To: gmx-users@gromacs.org Subject: [gmx-users] How to make a lipid bilayer with specific dimensions? I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC). Therefore: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 will give you a bilayer that gets solvated with a water defect around the edges of the initial unit cell and that, after 10 - 200 ns of simulation, gives you an equilibrated bilayer (without water defect) that is much smaller than x=9.6, y=9.5. To get what you want, you need to either start your bilayer with larger x and y (calculate area per lipid in 9.6*9.5 to figure out how many lipids you should have and keep running genbox until you get that), or perhaps a run through inflategro might do it. Chris. --original message -- [gmx-users] How to make a lipid bilayer with specific dimensions? Justin A. Lemkul jalemkul at vt.edu Mon Sep 27 13:00:32 CEST 2010 * Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] NG HUI WEN wrote: Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman?s website 2) Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm) My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I Too big? If you're using either of the two coordinate files above (popc128a.pdb, popcx2.pdb), they should be too small. would like to ?crop? the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before. Do I have to use other software to achieve this? If so, I?d really appreciate some pointers. You can do this in three steps. If your goal is to have a single lipid bilayer in the middle of the box, with water around it: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14 genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb The reason you need three steps is that if you supply a z-dimension of 14 in the first genbox command, at least two full bilayers (or some fraction close to it) will be placed in your box. If that's your goal, then this can be done in one step. -Justin Thanks! Email has been scanned for viruses by UNMC email management service http://www.nottingham.edu.my -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
RE: [gmx-users] How to make a lipid bilayer with specific dimensions?
Points noted, thanks Justin! -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, September 28, 2010 10:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to make a lipid bilayer with specific dimensions? NG HUI WEN wrote: Thanks for that guys! I will try them out. Just a quick question here with regards to my lipids being possibly too small, does it have something to do with the minimum image criterion for PBC? I have ensured that the distance of edge of the box and the atoms at the side of the protein to be greater than the cutoff of 1.2nm (PME is used)... in the hope that the protein would not interact with it's neighbouring image. I hope I'm not going down the wrong direction in my understanding of pbc... Thanks!!! There is no direct relationship between genbox and the minimum image convention. You certainly need to build a system that is of sufficient size to avoid spurious PBC interactions, but when genbox does is independent of this fact. The problem is that genbox will not place a molecule that falls partially outside the box, thus deleting an entire lipid and leaving a gap at the edge of the box. Like Chris said, this can lead to your system compressing somewhat to give dimensions smaller than what you were hoping for. Whether or not this is a problem in the long run is up to you to decide based on the specifics of your system. Short answer: make your box slightly larger than you think you need and equilibrate for a long time to ensure that your box is stable. -Justin -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca Sent: Monday, September 27, 2010 8:30 PM To: gmx-users@gromacs.org Subject: [gmx-users] How to make a lipid bilayer with specific dimensions? I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC). Therefore: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 will give you a bilayer that gets solvated with a water defect around the edges of the initial unit cell and that, after 10 - 200 ns of simulation, gives you an equilibrated bilayer (without water defect) that is much smaller than x=9.6, y=9.5. To get what you want, you need to either start your bilayer with larger x and y (calculate area per lipid in 9.6*9.5 to figure out how many lipids you should have and keep running genbox until you get that), or perhaps a run through inflategro might do it. Chris. --original message -- [gmx-users] How to make a lipid bilayer with specific dimensions? Justin A. Lemkul jalemkul at vt.edu Mon Sep 27 13:00:32 CEST 2010 * Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] NG HUI WEN wrote: Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman?s website 2) Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm) My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I Too big? If you're using either of the two coordinate files above (popc128a.pdb, popcx2.pdb), they should be too small. would like to ?crop? the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before. Do I have to use other software to achieve this? If so, I?d really appreciate some pointers. You can do this in three steps. If your goal is to have a single lipid bilayer in the middle of the box, with water around it: genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919 editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14 genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb The reason you need three steps is that if you supply a z-dimension of 14 in the first genbox command, at least two full bilayers (or some fraction close to it) will be placed in your box. If that's your goal, then this can be done in one step. -Justin Thanks! Email has been scanned for viruses by UNMC email management service
