[gmx-users] high temperature during mdrun
Hi dear gmx-usersI am simulating gold surface- protein interaction by GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun starts, temperature reaches to 5.50769e+05 and mdrun fails. md.mdp file containe: title = gold cpp = cpp include = ; RUN CONTROL PARAMETERS integrator = md comm_mode = Linear ;nstcomm = 1 ;comm_grps = Protein Non-protein ;nstcalcenergy = 1 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 500.0 emstep = 0.001 tinit = 0.000 dt = 0.0005 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 3000 nstvout = 3000 nstfout = 0 nstlog = 1 nstenergy = 3000 ; Output frequency and precision for xtc file nstxtcout = 3000 xtc-precision = 3000 ; NEIGHBORSEARCHING PARAMETERS ; Periodic boundary conditions: xyz (default), no (vacuum) pbc = xyz periodic_molecules = yes ; nblist cut-off rlist = 1.10 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME r_coulomb = 1.1 ;pme_order = 6 ;fourierspacing = 0.10 ewald_rtol = 1e-06 ewald_geometry = 3d ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.90 rvdw = 1.10 ; OPTIONS FOR BONDS constraints = none constraint-algorithm = Lincs lincs-order = 8 lincs-iter = 12 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 90 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = Nose-Hoover nhchainlength = 1 ; Groups to couple separately tc-grps = Protein SOL NA CL slab AUC ; Time constant (ps) and reference temperature (K) tau-t = 0.2 0.2 0.2 0.2 0.2 0.2 ref-t = 300 300 300 300 300 300 ; Non-equilibrium MD stuff freezegrps = slab freezedim = Y Y Y Can anyone help me to solve this problem?thank you in advance Fatemeh Ramezani -- 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.
[gmx-users] mdrun failure
Hi dear gmx-usersI am simulating gold surface- protein interaction by GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun starts, temperature reaches to 5.50769e+05. md.mdp file containe: title = gold cpp = cpp include = ; RUN CONTROL PARAMETERS integrator = md comm_mode = Linear ;nstcomm = 1 ;comm_grps = Protein Non-protein ;nstcalcenergy = 1 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 500.0 emstep = 0.001 tinit = 0.000 dt = 0.0005 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 3000 nstvout = 3000 nstfout = 0 nstlog = 1 nstenergy = 3000 ; Output frequency and precision for xtc file nstxtcout = 3000 xtc-precision = 3000 ; NEIGHBORSEARCHING PARAMETERS ; Periodic boundary conditions: xyz (default), no (vacuum) pbc = xyz periodic_molecules = yes ; nblist cut-off rlist = 1.10 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME r_coulomb = 1.1 ;pme_order = 6 ;fourierspacing = 0.10 ewald_rtol = 1e-06 ewald_geometry = 3d ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.90 rvdw = 1.10 ; OPTIONS FOR BONDS constraints = none constraint-algorithm = Lincs lincs-order = 8 lincs-iter = 12 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 90 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = Nose-Hoover nhchainlength = 1 ; Groups to couple separately tc-grps = Protein SOL NA CL slab AUC ; Time constant (ps) and reference temperature (K) tau-t = 0.2 0.2 0.2 0.2 0.2 0.2 ref-t = 300 300 300 300 300 300 ; Non-equilibrium MD stuff freezegrps = slab freezedim = Y Y Y Can anyone help me to solve this problem?thank you in advance Fatemeh Ramezani -- 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.
[gmx-users] mdrun failed
Hi dear gmx-usersI want to simulate gold surface - proteininteraction by GOLP-CHARMM forcefield. In md step, after 7 ps , without anyreason mdrun failed. md.mdp contains: title = gold cpp = cpp include = ; RUN CONTROL PARAMETERS integrator = md ;comm_mode = Linear ;nstcomm = 1 ;comm_grps = Protein non-Protein ;nstcalcenergy = 1 ; ENERGY MINIMIZATIONOPTIONS ; Force tolerance andinitial step-size emtol = 500.0 emstep = 0.001 tinit = 0.000 dt = 0.001 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 3000 nstvout = 3000 nstfout = 0 nstlog = 1 nstenergy = 3000 ;nsttcouple = 5 ; Output frequency andprecision for xtc file nstxtcout = 3000 xtc-precision = 3000 ; NEIGHBORSEARCHINGPARAMETERS ; Periodic boundaryconditions: xyz (default), no (vacuum) pbc = xyz periodic_molecules = yes ; nblistcut-off rlist = 1.10 ; OPTIONS FORELECTROSTATICS AND VDW ; Method for doingelectrostatics coulombtype = PME r_coulomb= 1.1 ;pme_order = 6 ;fourierspacing = 0.10 ewald_rtol = 1e-06 ewald_geometry = 3d ; Method for doing Vander Waals vdw-type= switch ; cut-offlengths rvdw-switch = 0.90 rvdw= 1.10 ; OPTIONS FORBONDS constraints = all-bonds constraint-algorithm= Lincs lincs-order = 8 lincs-iter = 12 ; Lincs will write awarning to the stderr if in one step a bond ; rotates over moredegrees than lincs-warnangle = 90 ; OPTIONS FOR WEAKCOUPLING ALGORITHMS ; Temperature coupling Tcoupl = Nose-Hoover nhchainlength = 1 ; Groups to coupleseparately tc-grps =ProteinNon-Protein ; Time constant (ps) andreference temperature (K) tau-t = 0.2 0.2 ref-t = 310 310 ; Non-equilibrium MDstuff freezegrps = slab freezedim = Y Y Y Fatemeh Ramezani mdrun command is: nohup mdrun -s md.tpr-o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin on -pinoffset 1 & the last line of md.log is: Step Time Lambda 7460 7.46000 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.39081e+04 1.47221e+04 3.15826e+03 -1.85050e+03 1.80904e+04 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential 2.97824e+05 2.17254e+12 -6.91585e+06 3.01612e+04 2.17254e+12 Kinetic En. Total Energy Conserved En. TemperaturePressure (bar) 7.71065e+14 7.73237e+14 9.41950e+16 2.61554e+11 2.41578e+12 Constr. rmsd 1.15453e-01 The last line of nohup.out is: Changing nstlist from10 to 40, rlist from 1.1 to 1.1 Using 1 MPI thread Using 3 OpenMP threads Applying core pinning offset 1 Setting the maximum number of constraint warnings to -1 Back Off! I just backed up fws_md3.trr to ./#fws_md3.trr.20# Back Off! I justbacked up traj_comp.xtc to ./#traj_comp.xtc.22# Back Off! I justbacked up md3.edr to ./#md3.edr.20# starting mdrun 'Protein in water' 10 steps, 100.0ps. Can you help me to prevent from mdrun failing? Thank you very much Fatemeh Ramezani -- 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.
[gmx-users] Fw: mdrun failure
Hi dear gmx-usersIwant to simulate gold surface - protein interaction by GOLP-CHARMM forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp contains: title = goldcpp =cppinclude = ;RUN CONTROL PARAMETERSintegrator = md ;ENERGY MINIMIZATION OPTIONSemtol = 500.0emstep = 0.001tinit = 0.000dt =0.001nsteps = 10 ;OUTPUT CONTROL OPTIONSnstxout = 3000nstvout = 3000nstfout = 0nstlog = 1nstenergy = 3000 ;Output frequency and precision for xtc filenstxtcout = 3000xtc-precision = 3000 ;NEIGHBORSEARCHING PARAMETERS;Periodic boundary conditions: xyz (default), no (vacuum)pbc =xyzperiodic_molecules = yesrlist = 1.10 ;OPTIONS FOR ELECTROSTATICS AND VDW;Method for doing electrostaticscoulombtype = PMEr_coulomb = 1.1ewald_rtol = 1e-06ewald_geometry = 3d ;Method for doing Van der Waalsvdw-type = switchrvdw-switch = 0.90rvdw = 1.10 ;OPTIONS FOR BONDS constraints = h-bondsconstraint-algorithm = Lincslincs-order = 8lincs-iter = 12;Lincs will write a warning to the stderr if in one step a bond;rotates over more degrees thanlincs-warnangle = 90 ;OPTIONS FOR WEAK COUPLING ALGORITHMS;Temperature coupling Tcoupl = Nose-Hoovernhchainlength = 1;Groups to couple separatelytc-grps = Protein Non-Protein;Time constant (ps) and reference temperature (K)tau-t = 0.2 0.2ref-t = 310 310 ;Non-equilibrium MD stufffreezegrps = slabfreezedim = Y Y Y mdrun command is: nohup mdrun -smd.tpr -o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin on -pinoffset 1 & the last line of md.logis: Step Time Lambda 7460 7.46000 0.0 Energies(kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.39081e+04 1.47221e+04 3.15826e+03 -1.85050e+03 1.80904e+04 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential 2.97824e+05 2.17254e+12 -6.91585e+06 3.01612e+04 2.17254e+12 KineticEn. Total Energy Conserved En. Temperature Pressure(bar) 7.71065e+14 7.73237e+14 9.41950e+16 2.61554e+11 2.41578e+12 Constr.rmsd 1.15453e-01 The last line ofnohup.out is: Changing nstlist from 10to 40, rlist from 1.1 to 1.1 Using 1 MPI threadUsing 3 OpenMP threadsApplying core pinningoffset 1Setting the maximumnumber of constraint warnings to -1 Back Off! I just backedup fws_md3.trr to ./#fws_md3.trr.20# Back Off! I just backedup traj_comp.xtc to ./#traj_comp.xtc.22# Back Off! I just backedup md3.edr to ./#md3.edr.20#starting mdrun 'Proteinin water'10 steps, 100.0 ps. Can you help me toprevent from mdrun failing?Thank you very much Fatemeh Ramezani -- 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.
[gmx-users] mdrun failure
Hi dear gmx-users Iwant to simulate gold surface - protein interaction by GOLP-CHARMM forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp contains: title = gold cpp =cpp include = ;RUN CONTROL PARAMETERS integrator = md ;ENERGY MINIMIZATION OPTIONS emtol = 500.0 emstep = 0.001 tinit = 0.000 dt =0.001 nsteps = 10 ;OUTPUT CONTROL OPTIONS nstxout = 3000 nstvout = 3000 nstfout = 0 nstlog = 1 nstenergy = 3000 ;Output frequency and precision for xtc file nstxtcout = 3000 xtc-precision = 3000 ;NEIGHBORSEARCHING PARAMETERS ;Periodic boundary conditions: xyz (default), no (vacuum) pbc =xyz periodic_molecules = yes rlist = 1.10 ;OPTIONS FOR ELECTROSTATICS AND VDW ;Method for doing electrostatics coulombtype = PME r_coulomb = 1.1 ewald_rtol = 1e-06 ewald_geometry = 3d ;Method for doing Van der Waals vdw-type = switch rvdw-switch = 0.90 rvdw = 1.10 ;OPTIONS FOR BONDS constraints = h-bonds constraint-algorithm = Lincs lincs-order = 8 lincs-iter = 12 ;Lincs will write a warning to the stderr if in one step a bond ;rotates over more degrees than lincs-warnangle = 90 ;OPTIONS FOR WEAK COUPLING ALGORITHMS ;Temperature coupling Tcoupl = Nose-Hoover nhchainlength = 1 ;Groups to couple separately tc-grps = Protein Non-Protein ;Time constant (ps) and reference temperature (K) tau-t = 0.2 0.2 ref-t = 310 310 ;Non-equilibrium MD stuff freezegrps = slab freezedim = Y Y Y mdrun command is: nohup mdrun -smd.tpr -o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin on -pinoffset 1 & the last line of md.logis: Step Time Lambda 7460 7.46000 0.0 Energies(kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.39081e+04 1.47221e+04 3.15826e+03 -1.85050e+03 1.80904e+04 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential 2.97824e+05 2.17254e+12 -6.91585e+06 3.01612e+04 2.17254e+12 KineticEn. Total Energy Conserved En. Temperature Pressure(bar) 7.71065e+14 7.73237e+14 9.41950e+16 2.61554e+11 2.41578e+12 Constr.rmsd 1.15453e-01 The last line ofnohup.out is: Changing nstlist from 10to 40, rlist from 1.1 to 1.1 Using 1 MPI thread Using 3 OpenMP threads Applying core pinningoffset 1 Setting the maximumnumber of constraint warnings to -1 Back Off! I just backedup fws_md3.trr to ./#fws_md3.trr.20# Back Off! I just backedup traj_comp.xtc to ./#traj_comp.xtc.22# Back Off! I just backedup md3.edr to ./#md3.edr.20# starting mdrun 'Proteinin water' 10 steps, 100.0 ps. Can you help me toprevent from mdrun failing? Thank you very much Fatemeh Ramezani -- 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.
[gmx-users] lincs warning
Dear gmx usersplease help me if you know how can I change lincs warning threshold in mdp file or in command? thank you Fatemeh Ramezani -- 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.
[gmx-users] Fw: lincs warnin threshold
Fatemeh Ramezani On Sunday, 12 March 2017, 20:16, fatemeh ramezani <fr_...@yahoo.com> wrote: Hi I have a system of protein-gold-ions-water to simulate. The force field which I use, is Golp-charmm. In this force field two au atoms with mass 0.5 and charge 0.3 (AUC) rotates around the main au atoms (with mass 196.967 and charge -0.3: AUS)that are freezed during the simulation. from the beginning of em step, I get LINCS-warning as follow: Step 10, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.355795, max 10.124834 (between atoms 23842 and 23841) bonds that rotated more than 90 degrees: atom 1 atom 2 angle previous, current, constraint length 23842 23841 171.40.0700 0.7787 0.0700 22137 22138 171.50.0700 0.7786 0.0700 21466 21465 133.50.0700 0.0996 0.0700 Step 10, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.196701, max 10.123523 (between atoms 22137 and 22138) bonds that rotated more than 90 degrees: atom 1 atom 2 angle previous, current, constraint length 22137 22138 171.50.0700 0.7786 0.0700 23770 23769 172.70.0700 0.7763 0.0700 When I checked the warning, I see the first warning is related to 2 AUC and AUS atoms.but according to the force field setting it is necessary to AUC atoms rotate around the AUS.How can change the lincs warning threshold? can you help me to solve the problem? Anybody may help me? Your suggestions would be appreciated. Thanks in advance. Sincerely, Fatemeh -- 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.
[gmx-users] lincs warnin threshold
Hi I have a system of protein-gold-ions-water to simulate. The force field which I use, is Golp-charmm. In this force field two au atoms with mass 0.5 and charge 0.3 (AUC) rotates around the main au atoms (with mass 196.967 and charge -0.3: AUS)that are freezed during the simulation. from the beginning of em step, I get LINCS-warning as follow: Step 10, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.355795, max 10.124834 (between atoms 23842 and 23841) bonds that rotated more than 90 degrees: atom 1 atom 2 angle previous, current, constraint length 23842 23841 171.40.0700 0.7787 0.0700 22137 22138 171.50.0700 0.7786 0.0700 21466 21465 133.50.0700 0.0996 0.0700 Step 10, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.196701, max 10.123523 (between atoms 22137 and 22138) bonds that rotated more than 90 degrees: atom 1 atom 2 angle previous, current, constraint length 22137 22138 171.50.0700 0.7786 0.0700 23770 23769 172.70.0700 0.7763 0.0700 When I checked the warning, I see the first warning is related to 2 AUC and AUS atoms.but according to the force field setting it is necessary to AUC atoms rotate around the AUS.How can change the lincs warning threshold? can you help me to solve the problem? Anybody may help me? Your suggestions would be appreciated. Thanks in advance. Sincerely, Fatemeh -- 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.
[gmx-users] free energy
Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file: title = n.pdb restraining cpp = /lib/cpp constraints = all-bonds constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 integrator = sd dt = 0.0008 nsteps = 250 nstcomm = 100 nstcalcenergy = 100 nstdhdl = 100 comm_mode = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.4 ;rlistlong = 2 coulombtype = PME rcoulomb = 1.4 rcoulomb-switch = 0.8 rvdw = 1 vdwtype = shift rvdw-switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Pressure coupling is on ;Pcoupl = berendsen Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 energygrps = Protein Sol freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y free-energy = yes couple-moltype = Protein2 init-lambda = 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = ALL_LAMBDAS$ As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each Lambda 1 ( or I should divide 8 ns between 7 Lambda)? In other words, the simulation time for each of the 7 lambda should be 8 ns or every lambda simulation time should be considered so that the total simulation time of lambdas be 8 ns? I hope I could correctly ask my question. I would greatly appreciate your response to my question. Fatemeh Ramezani -- 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.
[gmx-users] adding new residue
-1.3180 2 1 2 4 13 9 0.00 0.5523 3 1 2 4 15 9 0.00 -1.3556 1 1 2 4 15 9 180.00 1.1506 2 1 2 4 15 9 0.00 1.2343 3 1 2 9 14 9 180.00 0.5648 2 1 2 9 14 9 0.00 0.4937 3 1 5 7 8 9 180.00 2.6401 2 1 5 7 18 9 180.00 2.6401 2 1 5 15 4 9 0.00 0.5230 3 1 5 15 16 9 0.00 0.3891 3 1 5 15 17 9 0.00 0.3891 3 2 1 5 6 9 0.00 1.3389 1 2 1 5 6 9 180.00 -1.3180 2 2 1 5 6 9 0.00 0.5523 3 2 1 5 7 9 0.00 0.6276 3 2 1 5 15 9 0.00 -1.3556 1 2 1 5 15 9 180.00 1.1506 2 2 1 5 15 9 0.00 1.2343 3 2 4 15 5 9 0.00 0.5230 3 2 4 15 16 9 0.00 0.3891 3 2 4 15 17 9 0.00 0.3891 3 3 2 1 5 9 0.00 1.3389 1 3 2 1 5 9 180.00 -1.3180 2 3 2 1 5 9 0.00 0.5523 3 3 2 1 10 9 0.00 0.5941 1 3 2 1 10 9 180.00 -2.8995 2 3 2 1 10 9 0.00 0.6569 3 3 2 1 11 9 0.00 0.5941 1 3 2 1 11 9 180.00 -2.8995 2 3 2 1 11 9 0.00 0.6569 3 3 2 4 12 9 0.00 0.5941 1 3 2 4 12 9 180.00 -2.8995 2 3 2 4 12 9 0.00 0.6569 3 3 2 4 13 9 0.00 0.5941 1 3 2 4 13 9 180.00 -2.8995 2 3 2 4 13 9 0.00 0.6569 3 3 2 4 15 9 0.00 1.4477 1 3 2 4 15 9 180.00 -1.1088 2 3 2 4 15 9 0.00 0.5816 3 3 2 9 14 9 0.00 1.2468 1 3 2 9 14 9 180.00 -0.5774 2 3 2 9 14 9 0.00 0.7238 3 4 2 1 5 9 0.00 0.2134 1 4 2 1 5 9 180.00 1.4267 2 4 2 1 5 9 0.00 0.6945 3 4 2 1 10 9 0.00 1.3389 1 4 2 1 10 9 180.00 -1.3180 2 4 2 1 10 9 0.00 0.5523 3 4 2 1 11 9 0.00 1.3389 1 4 2 1 11 9 180.00 -1.3180 2 4 2 1 11 9 0.00 0.5523 3 4 2 9 14 9 180.00 0.5648 2 4 2 9 14 9 0.00 0.4937 3 4 15 5 6 9 0.00 0.5146 3 4 15 5 7 9 0.00 0.5230 3 5 1 2 9 9 0.00 -1.4393 1 5 1 2 9 9 180.00 3.6777 2 5 1 2 9 9 0.00 0.9958 3 5 15 4 12 9 0.00 0.5146 3 5 15 4 13 9 0.00 0.5146 3 6 5 1 10 9 0.00 0.5941 1 6 5 1 10 9 180.00 -2.8995 2 6 5 1 10 9 0.00 0.6569 3 6 5 1 11 9 0.00 0.5941 1 6 5 1 11 9 180.00 -2.8995 2 6 5 1 11 9 0.00 0.6569 3 6 5 7 8 9 0.00 -0.2218 3 6 5 7 18 9 0.00 -0.2218 3 6 5 15 16 9 0.00 0.5439 3 6 5 15 17 9 0.00 0.5439 3 7 5 1 10 9 0.00 -0.2929 3 7 5 1 11 9 0.00 -0.2929 3 7 5 15 16 9 0.00 0.5230 3 7 5 15 17 9 0.00 0.5230 3 8 7 5 15 9 180.00 1.2552 2 9 2 1 10 9 0.00 -1.3682 1 9 2 1 10 9 180.00 2.2426 2 9 2 1 10 9 0.00 0.5858 3 9 2 1 11 9 0.00 -1.3682 1 9 2 1 11 9 180.00 2.2426 2 9 2 1 11 9 0.00 0.5858 3 9 2 4 12 9 0.00 -1.3682 1 9 2 4 12 9 180.00 2.2426 2 9 2 4 12 9 0.00 0.5858 3 9 2 4 13 9 0.00 -1.3682 1 9 2 4 13 9 180.00 2.2426 2 9 2 4 13 9 0.00 0.5858 3 9 2 4 15 9 0.00 0.6276 3 10 1 5 15 9 0.00 1.4477 1 10 1 5 15 9 180.00 -1.1088 2 10 1 5 15 9 0.00 0.5816 3 11 1 5 15 9 0.00 1.4477 1 11 1 5 15 9 180.00 -1.1088 2 11 1 5 15 9 0.00 0.5816 3 12 4 15 16 9 0.00 0.5439 3 12 4 15 17 9 0.00 0.5439 3 13 4 15 16 9 0.00 0.5439 3 13 4 15 17 9 0.00 0.5439 3 15 5 7 18 9 180.00 1.2552 2 [ dihedrals ] ; ai aj ak al fu xi0 kxi xi0 kxi 1 2 5 10 2 0.00 0. 1 2 5 11 2 0.00 0. 2 4 1 9 2 0.00 0. 2 4 1 3 2 0.00 0. 5 7 1 15 2 0.00 0. 5 7 1 6 2 0.00 0. 7 8 5 18 2 0.00 107.1941 4 15 2 12 2 0.00 0. 4 12 2 13 2 0.00 0. 15 4 5 16 2 0.00 0. 15 4 5 17 2 0.00 0. #ifdef POSRES_LIGAND [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 2 1 1000 1000 1000 4 1 1000 1000 1000 5 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 #endif I added atomtypes section in .atp file. I added hydroxyprolin hydrogen data in hdb file. I dded [bonds], [angles], [dihedrals] and 2th [dihedrals] in ffbonded.itp file respectively in [ bondtypes ], [ anglestypes ], [dihedraltypes ] and 2th [dihedraltypes ].in the first grompp, this error appeared:number of coordinates in coordinate file (x.pdb, 72323) does not match topology (x.top, 95870) that the difference is equal to sol atom number that is 23547I dont know how can I solve this problem. I appreciate any help. Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting
[gmx-users] Fw: Add new residue to oplsaa force field
Dear JustinThanks for your tip, After I edit atomtype in ffbonded file problem solved. There is a new problem. I made hydroxyprolin top file by mktop and I added bond, angle and dihedral parameters to the ffbonded file. ; ; This topology was generated by MKTOP ; ; Please cite this work. ; Ribeiro, A.A.S.T.; Horta, B.A.C.; de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. ; MKTOP does not generate charges!!! You will need to take care of that yourself!! ; Check your topology!! Make sure the atom types make sense. #include /opt/bio/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp [ moleculetype ] ; Name nrexcl MOL 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_902 1 HYP N1 5 -0.14000 14.0067 2 opls_135 1 HYP C1 1 0.01000 12.011 3 opls_235 1 HYP C2 2 0.5 12.011 4 opls_281 1 HYP O1 2 -0.5 15.9994 5 opls_136 1 HYP C3 3 -0.12000 12.011 6 opls_158 1 HYP C4 4 -0.12000 12.011 7 opls_908 1 HYP C5 5 -0.05000 12.011 8 opls_154 1 HYP O2 4 -0.68300 15.9994 9 opls_140 1 HYP H1 1 0.06000 1.008 10 opls_140 1 HYP H2 3 0.06000 1.008 11 opls_140 1 HYP H3 3 0.06000 1.008 12 opls_140 1 HYP H4 4 0.06000 1.008 13 opls_155 1 HYP H5 4 0.06000 1.008 14 opls_140 1 HYP H6 5 0.06000 1.008 15 opls_140 1 HYP H7 5 0.06000 1.008 [ bonds ] 1 7 1 0.146 319657.6 1 2 1 0.147 319657.6 2 9 1 0.109 284512.0 2 5 1 0.154 224262.4 2 3 1 0.153 224262.4 3 4 1 0.122 20.0 5 11 1 0.109 284512.0 5 10 1 0.109 284512.0 5 6 1 0.150 224262.4 6 12 1 0.109 284512.0 6 8 1 0.141 267776.0 6 7 1 0.151 224262.4 7 15 1 0.109 284512.0 7 14 1 0.109 284512.0 8 13 1 0.096 462750.4 [ angles ] 1 7 6 1 103.026 470.281 1 7 15 1 113.597 292.880 1 7 14 1 109.458 292.880 1 2 9 1 114.712 292.880 1 2 5 1 103.936 470.281 1 2 3 1 108.272 669.440 2 1 7 1 110.799 433.462 2 5 11 1 113.386 313.800 2 5 10 1 109.493 313.800 2 5 6 1 103.337 488.273 2 3 4 1 120.399 200.000 3 2 9 1 106.795 418.400 3 2 5 1 112.252 585.760 5 2 9 1 110.968 313.800 5 6 12 1 113.836 313.800 5 6 8 1 108.872 418.400 5 6 7 1 103.268 488.273 6 5 11 1 113.403 313.800 6 5 10 1 109.458 313.800 6 8 13 1 109.466 460.240 6 7 15 1 113.577 313.800 6 7 14 1 109.490 313.800 7 6 12 1 113.170 313.800 7 6 8 1 109.597 418.400 8 6 12 1 107.964 292.880 10 5 11 1 107.676 276.144 14 7 15 1 107.597 276.144 [ dihedrals ] 2 1 7 6 3 2 1 7 15 3 2 1 7 14 3 7 1 2 9 3 7 1 2 5 3 7 1 2 3 3 1 2 5 11 3 9 2 5 11 3 3 2 5 11 3 1 2 5 10 3 9 2 5 10 3 3 2 5 10 3 1 2 5 6 3 9 2 5 6 3 3 2 5 6 3 1 2 3 4 3 9 2 3 4 3 5 2 3 4 3 2 5 6 12 3 11 5 6 12 3 10 5 6 12 3 2 5 6 8 3 11 5 6 8 3 10 5 6 8 3 2 5 6 7 3 11 5 6 7 3 10 5 6 7 3 5 6 8 13 3 12 6 8 13 3 7 6 8 13 3 5 6 7 1 3 12 6 7 1 3 8 6 7 1 3 5 6 7 15 3 12 6 7 15 3 8 6 7 15 3 5 6 7 14 3 12 6 7 14 3 8 6 7 14 3 [ dihedrals ] [ pairs ] 6 2 1 15 2 1 14 2 1 9 7 1 5 7 1 3 7 1 11 1 1 11 9 1 11 3 1 10 1 1 10 9 1 10 3 1 6 1 1 6 9 1 6 3 1 4 1 1 4 9 1 4 5 1 12 2 1 12 11 1 12 10 1 8 2 1 8 11 1 8 10 1 7 2 1 7 11 1 7 10 1 13 5 1 13 12 1 13 7 1 1 5 1 1 12 1 1 8 1 15 5 1 15 12 1 15 8 1 14 5 1 14 12 1 14 8 1 [ system ] ; Name MKTOP [ molecules ] ; Compound #mols MOL 1 As you can see in the topology file from mktop, there is no dihedral coefficients in the proper dihedral section that leads to creation of new error after grompp command. Why mktop doesn't produce these dihedral coefficient? and how can I solve it?Thanks in advance Fatemeh Ramezani -- 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.
[gmx-users] Add new residue to oplsaa force field
Dear JustinHydroxyprolin dihedral coefficients there are not in ffbonded file in oplsaa forcefield. I need to find it, and I add. I have Hydroxyprolin charmm parameters (dihedral parameters). How can I convert charmm dihedral parameters to oplsaa parameters?Can you help me so that I resolve this problem?Thanks for your guides Fatemeh Ramezani -- 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.
[gmx-users] Add new residue to forcefield
7 0.06 1.008 ; qtot 0.77 22 opls_140 23HYPHB2 7 0.06 1.008 ; qtot 0.83 23 opls_136 23HYP CG 8 -0.12 12.011 ; qtot 0.71 24 opls_140 23HYP HG 8 0.06 1.008 ; qtot 0.77 25 opls_167 23HYP OH 8 -0.68315.9994 ; qtot 0.087 26 opls_168 23HYP HO 8 0.435 1.008 ; qtot 0.522 27 opls_245 23HYP CD 9 -0.05 12.011 ; qtot 0.472 28 opls_140 23HYP HD 9 0.06 1.008 ; qtot 0.532 29 opls_235 23HYP C 100.5 12.011 ; qtot 1.032 30 opls_236 23HYP O 10 -0.515.9994 ; qtot 0.532 ; residue 24 GLY rtp GLY q -0.9 31 opls_238 24GLY N 11 -0.514.0067 ; qtot 0.032 32 opls_241 24GLY H 110.3 1.008 ; qtot 0.332 33 opls_298 24GLY CA 11 0.09 12.011 ; qtot 0.422 34 opls_140 24GLYHA1 11 0.06 1.008 ; qtot 0.482 35 opls_140 24GLYHA2 11 0.06 1.008 ; qtot 0.542 36 opls_271 24GLY C 120.7 12.011 ; qtot 1.242 37 opls_272 24GLY O1 12 -0.815.9994 ; qtot 0.442 38 opls_272 24GLY O2 12 -0.815.9994 ; qtot -0.358 . . . When I grompp, I get this error : ERROR 1 [file topol.top, line 258]: No default Angle types In topol.top line 258 contain atoms 25 23 27 that are atoms OH CG CD and I added the angle between them in [angletypes] section in ffbonded.itp file. I would be grateful if anyone could shed some light on the origin of this error, and on what I can do to correct it. Fatemeh Ramezani -- 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.
[gmx-users] graphene top file
Dear gmx-users I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with editconf command. Then I made top file with g_x2top command. But in top file connection between atoms is not correct(highlighted lines below). How can I solve this problem? Connection in pdb file for 12 atoms; CONECT12 CONECT213 CONECT324 CONECT43 CONECT56 CONECT657 CONECT768 CONECT87 CONECT9 10 CONECT 109 11 CONECT 11 10 12 Connection in top file for these atoms; [ bonds ] ; aiaj functc0c1c2c3 1 21 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1 61 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1 1936 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 2 31 1.42e-01 4.00e+05 1.42e-01 4.00e+05 281 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 3 41 1.42e-01 4.00e+05 1.42e-01 4.00e+05 384 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 4 71 1.42e-01 4.00e+05 1.42e-01 4.00e+05 485 1 1.41e-01 4.00e+05 1.41e-01 4.00e+05 5 61 1.42e-01 4.00e+05 1.42e-01 4.00e+05 510 1 1.41e-01 4.00e+05 1.41e-01 4.00e+05 5 1940 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 6 71 1.42e-01 4.00e+05 1.42e-01 4.00e+05 7 81 1.42e-01 4.00e+05 1.42e-01 4.00e+05 8111 1.41e-01 4.00e+05 1.41e-01 4.00e+05 8891 1.41e-01 4.00e+05 1.41e-01 4.00e+05 9101 1.42e-01 4.00e+05 1.42e-01 4.00e+05 9141 1.42e-01 4.00e+05 1.42e-01 4.00e+05 9 1944 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1011 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1112 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 Fatemeh Ramezani -- 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.
[gmx-users] In itp file from prodrg, what is C0 and C1 in bonds, angles and dihedrals section
Hi Dear gmx-users In itp file from prodrg, what is C0 and C1 in bonds, angles and dihedrals section; [ bonds ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... Thank you Fatemeh Ramezani -- 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.
[gmx-users] boron atom parameter
Dear gmx users I am performing a simulation by gromacs. My ligand molecule has a boron atom and by topology builder softwares such as prodrg, ATB, swiss param, antechamber I get an error that boron atom is not supported by this program. Do you have any propose for solute this problem? How can I build a top file for this ligand? regards Fatemeh Ramezani -- 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.
[gmx-users] (no subject)
Dear Users I run this command: nohup mpirun -np 8 mdrun_mpi -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr Despite the use of nohup and , mdrun will stop after closing the putty window. Can anyone help me to solve this problem? thank you in advance -- 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.
[gmx-users] Mdrun kill despite the use of nohup
Dear Users I run this command: nohup mpirun -np 8 mdrun_mpi -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr Despite the use of nohup and , mdrun will stop after closing the putty window. Can anyone help me to solve this problem? thank you in advance -- 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.
[gmx-users] aptamer
Hi Dear gmx-users I want to simulate interaction of a DNA aptamer with a protein. I have aptamer sequence but I need a software or online server that correctly fold this single strand DNA sequence to a circular aptamer and give me the xyz or pdb format of folded structure. Can anyone help me? Fatemeh Ramezani -- 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.
[gmx-users] Is viscosity increasing in the system due to the protein unfolding?
Dear Gromacs users I performed a simulation about the protein adsorption on the gold surface. Protein fluctuation increased and it denatured after 10 ns simulation. By calculating the viscosity of system by g_energy -f x.edr -o visc.xvg, I founded that viscosity is increasing during the simulation. Due to the fact that by unfolding of protein its viscosity increase, can I relate the viscosity arising to the unfolding of protein? Fatemeh Ramezani -- 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.
