Re: [gmx-users] atoms are not part of any of the T-Coupling groups
gmxcheck of my index file gives: Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 2230 12230 1 Protein 2226 12226 2 Protein-H 2226 12226 3 C-alpha 308 32218 4 Backbone 922 12219 5 MainChain 1232 12226 6 MainChain+Cb1488 12226 7 MainChain+H 1232 12226 8 SideChain994 82225 9 SideChain-H 994 82225 10 Prot-Masses 2226 12226 11 non-Protein422272230 12 Ion422272230 13 CU 222272229 14 ZN 222282230 15 r_131__chA8 956 963 16 r_131__chB820692076 17 r_132 1112071217 18 r_286 1126112621 19 CA_chA_r131112091209 20 CA_chB_r131126132613 and following are the contents of my .mdp file: title = Umbrella pulling simulation define = -DPOSRES_CA_chA_r131 ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = CA_chA_r131 pull_group1 = CA_chB_r131 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 4200 ; kJ mol^-1 nm^-2 Thanks in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. The error is not a result of the #include mechanism; it's a problem in the group definitions, either in the .mdp file or in the index file. Without the full text of the .mdp and the gmxcheck output of the index.ndx file, there's little to suggest. -Justin --
Re: [gmx-users] atoms are not part of any of the T-Coupling groups
On 8/7/14, 12:16 AM, Nidhi Katyal wrote: gmxcheck of my index file gives: It looks like you have created the index file before adding any solvent. Hence you have 215000+ atoms that are not accounted for. You need to generate index files after the system is complete. You can, of course, re-use your custom groups, but they need to be used in addition to sensible groups for everything else. -Justin Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 2230 12230 1 Protein 2226 12226 2 Protein-H 2226 12226 3 C-alpha 308 32218 4 Backbone 922 12219 5 MainChain 1232 12226 6 MainChain+Cb1488 12226 7 MainChain+H 1232 12226 8 SideChain994 82225 9 SideChain-H 994 82225 10 Prot-Masses 2226 12226 11 non-Protein422272230 12 Ion422272230 13 CU 222272229 14 ZN 222282230 15 r_131__chA8 956 963 16 r_131__chB820692076 17 r_132 1112071217 18 r_286 1126112621 19 CA_chA_r131112091209 20 CA_chB_r131126132613 and following are the contents of my .mdp file: title = Umbrella pulling simulation define = -DPOSRES_CA_chA_r131 ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = CA_chA_r131 pull_group1 = CA_chB_r131 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 4200 ; kJ mol^-1 nm^-2 Thanks in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using
[gmx-users] atoms are not part of any of the T-Coupling groups
Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atoms are not part of any of the T-Coupling groups
On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. The error is not a result of the #include mechanism; it's a problem in the group definitions, either in the .mdp file or in the index file. Without the full text of the .mdp and the gmxcheck output of the index.ndx file, there's little to suggest. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
