Re: [gmx-users] question about the output of minimization
On 7/11/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Yes I tried the command you wrote but it is still in the corner of the box. Is there anything else I can do? The coordinates I used to center the protein are the ones which are in the last line of the .gro file. The last line of the .gro file are the box vectors, not the center of the system, so you are not, in fact, centering the protein. You are placing it in the corner of the box yourself. The -center option overrides the -c option. If you want the protein centered, omit -center in your editconf command. -Justin Thank you On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Or not? Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite system is an arbitrary location; you have to re-wrap the unit cell to achieve the expected outcome. It's centered, it just may not look like it in the current representation. -Justin On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? It's a triclinic representation of the unit cell. Nothing is wrong. My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Is a dodecahedral box appropriate for a protein in a membrane? The inherent symmetry of a slab of any sort dictates that you should be using a cubic or rectangular box. Dodecahedral and octahedral boxes are better for systems with spherical symmetry, like globular proteins in water. I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -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 -- 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 -- 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 * Onl
Re: [gmx-users] question about the output of minimization
Yes I tried the command you wrote but it is still in the corner of the box. Is there anything else I can do? The coordinates I used to center the protein are the ones which are in the last line of the .gro file. Thank you > > > On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> ah okey. Thank you. >> And I have another question. Why is the protein in the corner of the box >> and not in the middle? >> I thought I centered it with the command: >> >> editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 >> 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut >> >> Or not? >> > > Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite > system > is an arbitrary location; you have to re-wrap the unit cell to achieve the > expected outcome. It's centered, it just may not look like it in the > current > representation. > > -Justin > >>> >>> >>> On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? >>> >>> It's a triclinic representation of the unit cell. Nothing is wrong. >>> My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut >>> >>> Is a dodecahedral box appropriate for a protein in a membrane? The >>> inherent >>> symmetry of a slab of any sort dictates that you should be using a >>> cubic >>> or >>> rectangular box. Dodecahedral and octahedral boxes are better for >>> systems >>> with >>> spherical symmetry, like globular proteins in water. >>> I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? >>> >>> There is no box shift; it's just a visual representation of the >>> dodecahedral >>> box. You can "correct" it (for visualization purposes) by running >>> trjconv >>> -pbc >>> mol -ur compact. >>> >>> -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 >>> >> >> >> > > -- > > > 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 po
Re: [gmx-users] question about the output of minimization
On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Or not? Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite system is an arbitrary location; you have to re-wrap the unit cell to achieve the expected outcome. It's centered, it just may not look like it in the current representation. -Justin On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? It's a triclinic representation of the unit cell. Nothing is wrong. My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Is a dodecahedral box appropriate for a protein in a membrane? The inherent symmetry of a slab of any sort dictates that you should be using a cubic or rectangular box. Dodecahedral and octahedral boxes are better for systems with spherical symmetry, like globular proteins in water. I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -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 -- 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] question about the output of minimization
Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Or not? > > > On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I did a minimization of my structure. But the output seems a bit strange >> for me, since my input was the protein with its membrane in a box like >> this: >> # = box P = Protein M=Membrane >> >> >> # >> # # >> # MM# >> # # >> # # >> # # >> # >> >> But the output of the minimization looks like this >> >> # >> ## >> #M M # >># # >> ## >> ## >> ## >> >> How can that be? > > It's a triclinic representation of the unit cell. Nothing is wrong. > >> My box was created with: >> >> editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 >> 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut >> > > Is a dodecahedral box appropriate for a protein in a membrane? The > inherent > symmetry of a slab of any sort dictates that you should be using a cubic > or > rectangular box. Dodecahedral and octahedral boxes are better for systems > with > spherical symmetry, like globular proteins in water. > >> >> I put solvent in it with: >> >> genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro >> 2>>logErr 1>>logOut >> >> >> The mdp file for the minimization looks like this: >> >> define = -DPOSRES >> integrator = steep >> emtol = 10 >> nsteps = 1500 >> nstenergy = 1 >> energygrps = System >> coulombtype = PME >> rcoulomb= 0.9 >> rvdw= 0.9 >> rlist = 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> pbc = xyz >> >> >> Can you please tell me how I can prevent my box to shift? >> > > There is no box shift; it's just a visual representation of the > dodecahedral > box. You can "correct" it (for visualization purposes) by running trjconv > -pbc > mol -ur compact. > > -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] question about the output of minimization
On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? It's a triclinic representation of the unit cell. Nothing is wrong. My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Is a dodecahedral box appropriate for a protein in a membrane? The inherent symmetry of a slab of any sort dictates that you should be using a cubic or rectangular box. Dodecahedral and octahedral boxes are better for systems with spherical symmetry, like globular proteins in water. I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -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] question about the output of minimization
Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? Thank you, Eva -- 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
