[gmx-users] about tabulated potentials
I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- 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] about tabulated potentials
From your system information, I understand that you need to specify tabulated potentials between atoms P and P, and between atoms C and P, and so on. To achieve this, you need to create energy groups with atom types P and C, and specify energygrp_table options in the grompp such as following energygrps = P C ; (and rest of the groups in your system, you will need to specify index file containing energy groups ) energygrp_table = P P P C so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run directory, and uses it for P-P and P-C interactions, whereas for all other interactions default table.xvg file is used. I hope this helps. Regards Sikandar On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang liu4...@gmail.com wrote: I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- 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 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] about tabulated potentials
Thanks for help. If I have more atoms and they can interact each other or itself, like PP, PC, PN, CP, CN, CC How's the energygrp_table looking like? I know there should be a option in the grompp, but how to do that? And how to generate the index file? I am sorry for so many questions, I am really not familiar with it. On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak symasha...@gmail.comwrote: From your system information, I understand that you need to specify tabulated potentials between atoms P and P, and between atoms C and P, and so on. To achieve this, you need to create energy groups with atom types P and C, and specify energygrp_table options in the grompp such as following energygrps = P C ; (and rest of the groups in your system, you will need to specify index file containing energy groups ) energygrp_table = P P P C so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run directory, and uses it for P-P and P-C interactions, whereas for all other interactions default table.xvg file is used. I hope this helps. Regards Sikandar On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang liu4...@gmail.com wrote: I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- 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 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 -- Best, Liang Liu -- 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] about tabulated potentials
On 16/11/2011 2:45 PM, Liu, Liang wrote: Thanks for help. If I have more atoms and they can interact each other or itself, like PP, PC, PN, CP, CN, CC How's the energygrp_table looking like? I know there should be a option in the grompp, but how to do that? See manual sections 7.3.12 and 6.7.2. And how to generate the index file? I am sorry for so many questions, I am really not familiar with it. http://www.gromacs.org/Documentation/File_Formats/Index_File Mark On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak symasha...@gmail.com mailto:symasha...@gmail.com wrote: From your system information, I understand that you need to specify tabulated potentials between atoms P and P, and between atoms C and P, and so on. To achieve this, you need to create energy groups with atom types P and C, and specify energygrp_table options in the grompp such as following energygrps = P C ; (and rest of the groups in your system, you will need to specify index file containing energy groups ) energygrp_table = P P P C so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run directory, and uses it for P-P and P-C interactions, whereas for all other interactions default table.xvg file is used. I hope this helps. Regards Sikandar On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang liu4...@gmail.com mailto:liu4...@gmail.com wrote: I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] about tabulated potentials
Thanks, I will try to figure it out. On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/11/2011 2:45 PM, Liu, Liang wrote: Thanks for help. If I have more atoms and they can interact each other or itself, like PP, PC, PN, CP, CN, CC How's the energygrp_table looking like? I know there should be a option in the grompp, but how to do that? See manual sections 7.3.12 and 6.7.2. And how to generate the index file? I am sorry for so many questions, I am really not familiar with it. http://www.gromacs.org/Documentation/File_Formats/Index_File Mark On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak symasha...@gmail.comwrote: From your system information, I understand that you need to specify tabulated potentials between atoms P and P, and between atoms C and P, and so on. To achieve this, you need to create energy groups with atom types P and C, and specify energygrp_table options in the grompp such as following energygrps = P C ; (and rest of the groups in your system, you will need to specify index file containing energy groups ) energygrp_table = P P P C so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run directory, and uses it for P-P and P-C interactions, whereas for all other interactions default table.xvg file is used. I hope this helps. Regards Sikandar On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang liu4...@gmail.com wrote: I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- 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 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 -- Best, Liang Liu -- 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 -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org
