[gmx-users] umbrella sampling-Bimodal Histograms
Hi Friends, When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? Thanks, -- Aswathy -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energy calculation
hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is ; VARIOUS PREPROCESSING OPTIONStitle = Yocpp = /usr/bin/cppinclude = define = ; RUN CONTROL PARAMETERSintegrator = md; Start time and timestep in pstinit = 0dt = 0.001nsteps = 50; For exact run continuation or redoing part of a runinit_step = 0; mode for center of mass motion removalcomm-mode = Linear; number of steps for center of mass motion removalnstcomm = 1; group(s) for center of mass motion removalcomm-grps = ; ENERGY MINIMIZATION OPTIONS; Force tolerance and initial step-sizeemtol = 10emstep = 0.01; Max number of iterations in relax_shellsniter = 20; Step size (1/ps^2) for minimization of flexible constraintsfcstep = 0; Frequency of steepest descents steps when doing CGnstcgsteep = 1000nbfgscorr = 10 ; NEIGHBORSEARCHING PARAMETERS; nblist update frequencynstlist = 5; ns algorithm (simple or grid)ns_type = grid; Periodic boundary conditions: xyz (default), no (vacuum); or full (infinite systems only)pbc = xyz; nblist cut-off rlist = 1.5domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostaticscoulombtype = PMErcoulomb-switch = 0rcoulomb = 1.5; Dielectric constant (DC) for cut-off or DC of reaction fieldepsilon-r = 1; Method for doing Van der Waalsvdw-type = Cut-off; cut-off lengths rvdw-switch = 0rvdw = 1.5; Apply long range dispersion corrections for Energy and PressureDispCorr = EnerPres; Extension of the potential lookup tables beyond the cut-offtable-extension = 1; Spacing for the PME/PPPM FFT gridfourierspacing = 0.12; FFT grid size, when a value is 0 fourierspacing will be usedfourier_nx = 0fourier_ny = 0fourier_nz = 0; EWALD/PME/PPPM parameterspme_order = 4ewald_rtol = 1e-05ewald_geometry = 3depsilon_surface = 0optimize_fft = no ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS; Temperature coupling Tcoupl = nose-hoover; Groups to couple separatelytc-grps = System; Time constant (ps) and reference temperature (K)tau_t = 0.1ref_t = 298; Pressure coupling Pcoupl = BerendsenPcoupltype = isotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau_p = 1compressibility = 4.5e-5ref_p = 1.0; Random seed for Andersen thermostatandersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic)annealing = no; Number of time points to use for specifying annealing in each groupannealing_npoints = ; List of times at the annealing points for each groupannealing_time = ; Temp. at each annealing point, for each group.annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUNgen_vel = yesgen_temp = 300gen_seed = 1993 ; OPTIONS FOR BONDS constraints = all-bonds; Type of constraint algorithmconstraint-algorithm = Lincs; Do not constrain the start configurationunconstrained-start = no; Use successive overrelaxation to reduce the number of shake iterationsShake-SOR = no; Relative tolerance of shakeshake-tol = 1e-04; Highest order in the expansion of the constraint coupling matrixlincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for; normal simulations, but use 2 to conserve energy in NVE runs.; For energy minimization with constraints it should be 4 to 8.lincs-iter = 1; Lincs will write a warning to the stderr if in one step a bond; rotates over more degrees thanlincs-warnangle = 30; Convert harmonic bonds to morse potentialsmorse = no ; ENERGY GROUP EXCLUSIONS; Pairs of energy groups for which all non-bonded interactions are excludedenergygrp_excl = the top file is [ defaults ]; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no
Re: [gmx-users] Energy miscalculation
i did three simulations 1) leaving the top file as it is above2) deleting the [pairs] and all the lines below3) deleting only the last line of the [pairs] the results with usage of the command gmxdump -s topol.tpr | lessfor step 0 are below 1)leaving the top file as it is above I)from md.log Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 5.70628e+00 8.37083e+00 6.80805e-03 1.72679e+02 -3.25801e+00 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28661e+01 3.94838e+01 Total Energy Temperature Pressure (bar) Cons. rmsd () 7.23499e+01 3.65291e+02 4.25495e+01 3.43881e-07 II) from gmxdump ffparams: atnr=5 ntypes=41 functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.5205e-05 functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[4]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05 functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[9]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07 functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[14]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06 functype[19]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[20]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[21]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[22]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[23]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[24]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02 functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02 functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02 functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02 functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02 functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01, rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00, rbcB[3]=-2.63176327e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01, rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01, rbcB[3]=-2.56062469e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00, rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00, rbcB[3]=-1.85645523e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01, rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00, rbcB[3]=-3.34730682e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00, rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01, rbcB[3]=-6.25015497e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[35]=LJ14, c6A= 0.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+00
[gmx-users] Re: Energy miscalculation
3) deleting only the last line of the [pairs] I)from md.log Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 5.70628e+00 8.37083e+00 0.0e+00 1.72679e+02 -3.25801e+00 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28593e+01 3.94837e+01 Total Energy Temperature Pressure (bar) Cons. rmsd () 7.23430e+01 3.65290e+02 4.25425e+01 3.43881e-07 II) from gmxdump ffparams: atnr=5 ntypes=40 functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.5205e-05 functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[4]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05 functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[9]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07 functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[14]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06 functype[19]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[20]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[21]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[22]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[23]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[24]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02 functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02 functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02 functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02 functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02 functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01, rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00, rbcB[3]=-2.63176327e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01, rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01, rbcB[3]=-2.56062469e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00, rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00, rbcB[3]=-1.85645523e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01, rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00, rbcB[3]=-3.34730682e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00, rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01, rbcB[3]=-6.25015497e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[35]=LJ14, c6A= 0.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+00 functype[36]=CONSTR, dA= 1.5399e-01, dB= 1.5399e-01 functype[37]=CONSTR, dA= 9.4478e-02, dB= 9.4478e-02 functype[38]=CONSTR, dA= 1.4307e-01, dB= 1.4307e-01 functype[39]=CONSTR, dA=
[gmx-users] Energy miscalculation
hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is ; VARIOUS PREPROCESSING OPTIONStitle = Yocpp = /usr/bin/cppinclude = define = ; RUN CONTROL PARAMETERSintegrator = md; Start time and timestep in pstinit = 0dt = 0.001nsteps = 50; For exact run continuation or redoing part of a runinit_step = 0; mode for center of mass motion removalcomm-mode = Linear; number of steps for center of mass motion removalnstcomm = 1; group(s) for center of mass motion removalcomm-grps = ; ENERGY MINIMIZATION OPTIONS; Force tolerance and initial step-sizeemtol = 10emstep = 0.01; Max number of iterations in relax_shellsniter = 20; Step size (1/ps^2) for minimization of flexible constraintsfcstep = 0; Frequency of steepest descents steps when doing CGnstcgsteep = 1000nbfgscorr = 10 ; NEIGHBORSEARCHING PARAMETERS; nblist update frequencynstlist = 5; ns algorithm (simple or grid)ns_type = grid; Periodic boundary conditions: xyz (default), no (vacuum); or full (infinite systems only)pbc = xyz; nblist cut-off rlist = 1.5domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostaticscoulombtype = PMErcoulomb-switch = 0rcoulomb = 1.5; Dielectric constant (DC) for cut-off or DC of reaction fieldepsilon-r = 1; Method for doing Van der Waalsvdw-type = Cut-off; cut-off lengths rvdw-switch = 0rvdw = 1.5; Apply long range dispersion corrections for Energy and PressureDispCorr = EnerPres; Extension of the potential lookup tables beyond the cut-offtable-extension = 1; Spacing for the PME/PPPM FFT gridfourierspacing = 0.12; FFT grid size, when a value is 0 fourierspacing will be usedfourier_nx = 0fourier_ny = 0fourier_nz = 0; EWALD/PME/PPPM parameterspme_order = 4ewald_rtol = 1e-05ewald_geometry = 3depsilon_surface = 0optimize_fft = no ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS; Temperature coupling Tcoupl = nose-hoover; Groups to couple separatelytc-grps = System; Time constant (ps) and reference temperature (K)tau_t = 0.1ref_t = 298; Pressure coupling Pcoupl = BerendsenPcoupltype = isotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau_p = 1compressibility = 4.5e-5ref_p = 1.0; Random seed for Andersen thermostatandersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic)annealing = no; Number of time points to use for specifying annealing in each groupannealing_npoints = ; List of times at the annealing points for each groupannealing_time = ; Temp. at each annealing point, for each group.annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUNgen_vel = yesgen_temp = 300gen_seed = 1993 ; OPTIONS FOR BONDS constraints = all-bonds; Type of constraint algorithmconstraint-algorithm = Lincs; Do not constrain the start configurationunconstrained-start = no; Use successive overrelaxation to reduce the number of shake iterationsShake-SOR = no; Relative tolerance of shakeshake-tol = 1e-04; Highest order in the expansion of the constraint coupling matrixlincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for; normal simulations, but use 2 to conserve energy in NVE runs.; For energy minimization with constraints it should be 4 to 8.lincs-iter = 1; Lincs will write a warning to the stderr if in one step a bond; rotates over more degrees thanlincs-warnangle = 30; Convert harmonic bonds to morse potentialsmorse = no ; ENERGY GROUP EXCLUSIONS; Pairs of energy groups for which all non-bonded interactions are excludedenergygrp_excl = the top file is [ defaults ]; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no
[gmx-users] Re: Energy miscalculation
1)leaving the top file as it is above I)from md.log Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 5.70628e+00 8.37083e+00 6.80805e-03 1.72679e+02 -3.25801e+00 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28661e+01 3.94838e+01 Total Energy Temperature Pressure (bar) Cons. rmsd () 7.23499e+01 3.65291e+02 4.25495e+01 3.43881e-07 II) from gmxdump ffparams: atnr=5 ntypes=41 functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.5205e-05 functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[4]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05 functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[9]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07 functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[14]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06 functype[19]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[20]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[21]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[22]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[23]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[24]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02 functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02 functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02 functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02 functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02 functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01, rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00, rbcB[3]=-2.63176327e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01, rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01, rbcB[3]=-2.56062469e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00, rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00, rbcB[3]=-1.85645523e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01, rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00, rbcB[3]=-3.34730682e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00, rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01, rbcB[3]=-6.25015497e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[35]=LJ14, c6A= 0.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+00 functype[36]=LJC14_Q, fqq= 0.e+00, qi= 0.e+00, qj= 0.e+00, c6= 0.e+00, c12= 3.32578907e-07 functype[37]=CONSTR, dA= 1.5399e-01, dB= 1.5399e-01 functype[38]=CONSTR, dA= 9.4478e-02
[gmx-users] Re: Energy miscalculation
3) deleting only the last line of the [pairs] I)from md.log Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 5.70628e+00 8.37083e+00 0.0e+00 1.72679e+02 -3.25801e+00 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28593e+01 3.94837e+01 Total Energy Temperature Pressure (bar) Cons. rmsd () 7.23430e+01 3.65290e+02 4.25425e+01 3.43881e-07 II) from gmxdump ffparams: atnr=5 ntypes=40 functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.5205e-05 functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[4]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05 functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[9]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07 functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[14]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06 functype[19]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[20]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[21]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[22]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[23]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[24]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02 functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02 functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02 functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02 functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02 functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01, rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00, rbcB[3]=-2.63176327e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01, rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01, rbcB[3]=-2.56062469e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00, rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00, rbcB[3]=-1.85645523e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01, rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00, rbcB[3]=-3.34730682e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00, rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01, rbcB[3]=-6.25015497e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[35]=LJ14, c6A= 0.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+00 functype[36]=CONSTR, dA= 1.5399e-01, dB= 1.5399e-01 functype[37]=CONSTR, dA= 9.4478e-02, dB= 9.4478e-02 functype[38]=CONSTR, dA= 1.4307e-01, dB= 1.4307e-01 functype[39]=CONSTR, dA= 1
[gmx-users] Re: Energy miscalculation
2) deleting the [pairs] and all the lines below I)from md.log Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ (SR) Disper. corr. Coulomb (SR) 5.70628e+00 8.37083e+00 -3.25801e+00 -7.32091e-03 -2.93587e+01 Coul. recip. Potential Kinetic En. Total Energy Temperature -1.21273e+02 -1.39819e+02 3.94033e+01 -1.00416e+02 3.64546e+02 Pressure (bar) Cons. rmsd () 3.09781e+01 3.89303e-07 II) from gmxdump ffparams: atnr=5 ntypes=39 functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.5205e-05 functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[4]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05 functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05 functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[9]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06 functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06 functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07 functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[14]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06 functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06 functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07 functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06 functype[19]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[20]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[21]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[22]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[23]=LJ_SR, c6= 0.e+00, c12= 0.e+00 functype[24]=LJ_SR, c6= 0.e+00, c12= 0.e+00functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02 functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02 functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02 functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02 functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02 functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01, rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00, rbcB[3]=-2.63176327e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01, rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01, rbcB[3]=-2.56062469e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00, rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00, rbcB[3]=-1.85645523e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01, rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00, rbcB[3]=-3.34730682e+01, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00, rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.e+00, rbcA[5]= 0.e+00rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01, rbcB[3]=-6.25015497e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00 functype[35]=CONSTR, dA= 1.5399e-01, dB= 1.5399e-01 functype[36]=CONSTR, dA= 9.4478e-02, dB= 9.4478e-02 functype[37]=CONSTR, dA= 1.4307e-01, dB= 1.4307e-01 functype[38]=CONSTR, dA= 1.4103e-01, dB= 1.4103e-01 fudgeQQ = 0.5 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s
[gmx-users] Re: Energy miscalculation
hi gmx-users sorry for this pack of emails. the page has not a good format. you can find my text included to this email. thanks hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 50 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy= 50 ; Output frequency and precision for xtc file nstxtcout= 100 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 298 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= no ; Number of time points to use for
[gmx-users] (no subject)
Hi all, I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager. I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job. Thanks a lot for any instruction. Bests, Amin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
Amin Arabbagheri wrote: Hi all, I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager. I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job. Thanks a lot for any instruction. Regarding grompp: http://www.gromacs.org/Documentation/FAQs As for mdrun, please provide your actual command line. The mdrun -np flag is nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np from which mdrun is launched. -Justin Bests, Amin -- 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
Use grompp normally, without the -np flag. Then run mdrun_mpi with your normal parameters as mpirun -np x mdrun_mpi -deffnm xx On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri wrote: > Hi all, > > I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic > package manager. > I want to run a simulation in parallel on a multi processor, single PC, but > to compile via grompp, it doesn't accept -np flag, and also , using -np in > mdrun, it still runs as a single job. > Thanks a lot for any instruction. > > Bests, > Amin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
Amin, the -np flag is not necessary any more for grompp in Gromacs 4.0. For mdrun, just use something like mpirun -np 4 mdrun -s topol.tpr Carsten On Jun 21, 2010, at 2:00 PM, Amin Arabbagheri wrote: > Hi all, > > I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package > manager. > I want to run a simulation in parallel on a multi processor, single PC, but > to compile via grompp, it doesn't accept -np flag, and also , using -np in > mdrun, it still runs as a single job. > Thanks a lot for any instruction. > > Bests, > Amin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Help with defining new residue (OXY--HEME)
Hi, I obtained parameters for a Morse potential between Oxygen molecule and Iron in heme (from ab initio calculations). How can I use this potential with the GROMOS96 parameters? I thought of a couple of options: 1) Define a new residue -- OXYHEM using the same parameters for HEME as in ffG43a1.rtp but just adding oxygen--heme interaction. (The problem with this is that the bonded interaction in the HEME uses the G96BOND, so, how would I maintain this G96BOND for all the atoms except the oxygen-Fe interaction for which I need to use the Morse potential). ** What are the steps needed to do this? *** 2. Is it possible to simply create an appropriate *.itp file to use in conjunction with the HEME already defined in the GROMOS96 files (*.atp, *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)? Any help will be appreciated. Thanks. o. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Help with defining new residue (OXY--HEME)
Omololu Akin-Ojo wrote: Hi, I obtained parameters for a Morse potential between Oxygen molecule and Iron in heme (from ab initio calculations). How can I use this potential with the GROMOS96 parameters? I thought of a couple of options: 1) Define a new residue -- OXYHEM using the same parameters for HEME as in ffG43a1.rtp but just adding oxygen--heme interaction. (The problem with this is that the bonded interaction in the HEME uses the G96BOND, so, how would I maintain this G96BOND for all the atoms except the oxygen-Fe interaction for which I need to use the Morse potential). ** What are the steps needed to do this? *** You could create an .rtp entry for this species and process it with pdb2gmx. I don't know how to put a Morse type bond in an .rtp file, but you can easily modify the resulting topology to include the proper term. 2. Is it possible to simply create an appropriate *.itp file to use in conjunction with the HEME already defined in the GROMOS96 files (*.atp, *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)? Sure, most things are possible :) See the manual, chapter 5. -Justin Any help will be appreciated. Thanks. o. -- 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/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/mailing_lists/users.php
Re: [gmx-users] Help with defining new residue (OXY--HEME)
Thanks, Justin. I appreciate this. I will go with the first option of creating a *.rtp file and manually change the subsequent *.top file to put in the morse potential. Thanks again. o. --- On Mon, 6/21/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Help with defining new residue (OXY--HEME) To: "Discussion list for GROMACS users" Date: Monday, June 21, 2010, 9:02 AM Omololu Akin-Ojo wrote: > Hi, > > I obtained parameters for a Morse potential between Oxygen molecule and Iron > in heme (from ab initio calculations). How can I use this potential with the > GROMOS96 parameters? > > I thought of a couple of options: > > 1) Define a new residue -- OXYHEM using the same parameters for HEME as in > ffG43a1.rtp but just adding oxygen--heme interaction. > (The problem with this is that the bonded interaction in the HEME uses the > G96BOND, so, how would I maintain this G96BOND for all the atoms except the > oxygen-Fe interaction for which I need to use the Morse potential). > ** What are the steps needed to do this? *** > You could create an .rtp entry for this species and process it with pdb2gmx. I don't know how to put a Morse type bond in an .rtp file, but you can easily modify the resulting topology to include the proper term. > 2. Is it possible to simply create an appropriate *.itp file to use in > conjunction with the HEME already defined in the GROMOS96 files (*.atp, > *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)? > Sure, most things are possible :) See the manual, chapter 5. -Justin > Any help will be appreciated. > > Thanks. > > o. > > -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energy miscalculation
Dear Thanasis: 8 posts on the same topic? I didn't even read them. If you want some help, I'd suggest that you start with a new subject line and post a single email containing all relevant information. You can see how it looks at the bottom of this list: http://lists.gromacs.org/pipermail/gmx-users/2010-June/date.html And perhaps you can imagine that many of us are a little hesitant to read 8 emails that may or may not be repeats of the same information. Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] umbrella sampling-Bimodal Histograms
Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] FEP for amino acid mutations
Dear Gromacs user, Still another problem... How can I manage the mutation upon a Trp? The mutation ALA-GLY does not cause any problem but the trasformation TRP-ALA seems uneasy. The Segmentation Fault error occurs suddenly I try to run the mdrun with lambda=1, with lambda=0.99 it take 6 step before to crash while if I start with lambda=0 it seems to work. So, I was thinking that it could be because the whole Trp rings, which loses lennard-jones interaction and charge, have still all its mass and this mass are connected on a single HB of the final alanine ( I'm using tha amber all-atom force field) that was the CG in the initial Trp. Could it be? Can how manage it somehow? Furthermore, if I change an aromatic residue in some long-sidechain amino acid how can I manage the dihedral and the bonds? I think I cannot let a bond disappear, for example if I try to transform a PHE in a LEU... Thank you for any hint you could give me! matteo > Date: Wed, 16 Jun 2010 15:17:30 +0200 > From: Matteo De Chiara > Subject: Re: [gmx-users] FEP for amino acid mutations. > To: gmx-users@gromacs.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Thank you! > I tried to change from Ala to Gly in aqueous environment and seems to > have worked well. Now I will try to change a Trp, the amino acid I > have to apply the real mutation. > > matteo > > > >> >> Message: 5 >> Date: Tue, 15 Jun 2010 08:53:25 +1000 >> From: "Dallas B. Warren" >> Subject: RE: [gmx-users] FEP for amino acid mutations. >> To: Discussion list for GROMACS users >> Message-ID: >> <89907ea1dcfb7548a431c13a270f9dd50ad84...@prk-exch-01.vcp.local> >> Content-Type: text/plain; charset=us-ascii >> >> I would make a new residue in the .rtp file. >> >> Catch ya, >> >> Dr. Dallas Warren >> Drug Delivery, Disposition and Dynamics >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@pharm.monash.edu.au >> +61 3 9903 9167 >> - >> When the only tool you own is a hammer, every problem begins to resemble >> a nail. >> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- >>> boun...@gromacs.org] On Behalf Of Matteo De Chiara >>> Sent: Monday, 14 June 2010 8:05 PM >>> To: gmx-users@gromacs.org >>> Subject: [gmx-users] FEP for amino acid mutations. >>> >>> Dear GROMACS users, >>> I would like to perform a FEP calculation mutating a residue outside >>> the active site of a protein. >>> I was wondering if I have to create a .itp file for the mutation or it >>> is possible to modify the .rtp file ( adding the state B parameter to >>> the amino acid I would like to change). Of course, in this case, I >>> will create a new amino acid type identical to the one I would like to >>> mutate in order to act only on the amino acid in a specific position. >>> >>> Thanks for your help! >>> >>> matteo >>> >>> >>> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] pull_pbcatom reporting strangely when set to 0
Hi,
I coded this and I looked at the code again.
pbcatom is always the global, system wide atom number.
But it seems that mdrun forgets to add one to the atom number
or maybe this is part of the mdrun output scheme of starting numbering at 0.
We would have to check this.
As far as I can see that is consistent with your results, right?
Berk
> Date: Sun, 20 Jun 2010 18:54:13 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull_pbcatom reporting strangely when set to 0
>
> Dear gromacs users:
>
> I am confused (again) about pull_pbcatom0. From this analysis, I am
> questioning if the pbcatom reported from grompp and in the top of the
> .log file is numerically defined *within* a group or in the context of
> the entire .gro file.
>
> Either way, I think that I have conclusively shown below that setting
> pull_pbcatomN to 0 is not reported properly. My hunch is that it is
> just a reporting problem and is working alright. For the reporting by
> grompp and at the beginning of mdrun, I think that the pbcatom is
> defined *within* a group, but that the selection of the pbcatom when
> setting pbcatom=0 is incorrect (sometimes drastically).
>
> I'm posting to the mailing list in the hopes that somebody can simply
> take a look at the relevant code and see where the problem is.
>
> Here, I have a .gro file that has protein, then lipid, then water. I
> have the lipid as pull group 0 and the protein as pull group 1.
> The protein has 14 atoms and the lipid group has 3456 atoms.
>
> These tests have all been run with 4.0.7 (and also 4.0.5 gives
> identical results).
>
> If I specify pull_pbcatom0=10 in my .mdp, then:
>
> grompp says:
> Pull group natoms pbc atom distance at start reference at t=0
> 0 345610
> 114 7 -0.000 0.000 -0.001 0.000 0.000 0.000
>
> and the .log file says:
> pull_group 0:
> atom (3456):
> atom[0,...,3455] = {14,...,3469}
> weight: not available
> pbcatom = 9
>
> This makes me think that at this stage the pull_pbcatom0 is defined
> within the group such that the accessible numebrs are [0,...,3455] --
> If this was not the case, then pbcatom0 should be reported as 9+14
> protein atoms = 25.
>
>
> Ok, so now I define pull_pbcatom0=0 in my .mdp, then:
>
> grompp says:
> Pull group natoms pbc atom distance at start reference at t=0
> 0 3456 1742
> 114 7 -0.000 0.000 -0.001 0.000 0.000 0.000
>
> and the .log file says:
> pull_group 0:
> atom (3456):
> atom[0,...,3455] = {14,...,3469}
> weight: not available
> pbcatom = 1741
>
> Which surprised me because 3456/2=1728 and 1728 -1 (use zero as first
> #) +14 (protein atoms) = 1741
>
> However, this suggests that at this stage the pull_pbcatom0 is defined
> in the context of the entire .gro file, not only within the group.
> This contradicts what I saw above.
>
>
> Next, I added a second protein (there are now 28 atoms of protein
> before the lipid coordinates start) and left pull_pbcatom0=0, now:
>
> grompp says:
> Pull group natoms pbc atom distance at start reference at t=0
> 0 3456 1756
> 12814 -0.000 0.000 -0.001 0.000 0.000 0.000
>
> and the .log file says:
> pull_group 0:
> atom (3456):
> atom[0,...,3455] = {28,...,3483}
> weight: not available
> pbcatom = 1755
>
> Where 1755 = 1741+14 so again it looks as if the pull_pbcatom0 is
> defined (or at least decided) in the context of the entire .gro file.
>
>
>
>
> Now I reverse the order of the protein and the lipid, with only one
> copy of the protein again.
> Here, I specify pull_pbcatom0=10 (pull group 0 remains the lipid):
>
> grompp says:
> Pull group natoms pbc atom distance at start reference at t=0
> 0 345610
> 114 3463 -0.000 0.000 -0.001 0.000 0.000 0.000
>
> and the .log file says:
> pull_group 0:
> atom (3456):
> atom[0,...,3455] = {0,...,3455}
> weight: not available
> pbcatom = 9
>
>
> Now I specify pull_pbcatom0=0
>
> grompp says:
> Pull group natoms pbc atom distance at start reference at t=0
> 0 3456 1728
> 114 3463 -0.000 0.000 -0.001 0.
[gmx-users] pull_pbcatom reporting strangely when set to 0
You're right, although I did not realize this at first. I got confused
(again) by the global numbering. Regarding the off-by-one numbering, I
can figure out what is meant there and that was not really my question.
Thanks Berk, and sorry for the confusion.
Chris.
I coded this and I looked at the code again.
pbcatom is always the global, system wide atom number.
But it seems that mdrun forgets to add one to the atom number
or maybe this is part of the mdrun output scheme of starting numbering at 0.
We would have to check this.
As far as I can see that is consistent with your results, right?
Berk
-- previous message --
Date: Sun, 20 Jun 2010 18:54:13 -0400
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] pull_pbcatom reporting strangely when set to 0
Dear gromacs users:
I am confused (again) about pull_pbcatom0. From this analysis, I am
questioning if the pbcatom reported from grompp and in the top of
the .log file is numerically defined *within* a group or in the
context of the entire .gro file.
Either way, I think that I have conclusively shown below that
setting pull_pbcatomN to 0 is not reported properly. My hunch is
that it is just a reporting problem and is working alright. For the
reporting by grompp and at the beginning of mdrun, I think that the
pbcatom is defined *within* a group, but that the selection of the
pbcatom when setting pbcatom=0 is incorrect (sometimes drastically).
I'm posting to the mailing list in the hopes that somebody can
simply take a look at the relevant code and see where the problem is.
Here, I have a .gro file that has protein, then lipid, then water. I
have the lipid as pull group 0 and the protein as pull group 1.
The protein has 14 atoms and the lipid group has 3456 atoms.
These tests have all been run with 4.0.7 (and also 4.0.5 gives
identical results).
If I specify pull_pbcatom0=10 in my .mdp, then:
grompp says:
Pull group natoms pbc atom distance at start reference at t=0
0 345610
114 7 -0.000 0.000 -0.001 0.000 0.000 0.000
and the .log file says:
pull_group 0:
atom (3456):
atom[0,...,3455] = {14,...,3469}
weight: not available
pbcatom = 9
This makes me think that at this stage the pull_pbcatom0 is defined
within the group such that the accessible numebrs are [0,...,3455]
-- If this was not the case, then pbcatom0 should be reported as
9+14 protein atoms = 25.
Ok, so now I define pull_pbcatom0=0 in my .mdp, then:
grompp says:
Pull group natoms pbc atom distance at start reference at t=0
0 3456 1742
114 7 -0.000 0.000 -0.001 0.000 0.000 0.000
and the .log file says:
pull_group 0:
atom (3456):
atom[0,...,3455] = {14,...,3469}
weight: not available
pbcatom = 1741
Which surprised me because 3456/2=1728 and 1728 -1 (use zero as
first #) +14 (protein atoms) = 1741
However, this suggests that at this stage the pull_pbcatom0 is
defined in the context of the entire .gro file, not only within the
group. This contradicts what I saw above.
Next, I added a second protein (there are now 28 atoms of protein
before the lipid coordinates start) and left pull_pbcatom0=0, now:
grompp says:
Pull group natoms pbc atom distance at start reference at t=0
0 3456 1756
12814 -0.000 0.000 -0.001 0.000 0.000 0.000
and the .log file says:
pull_group 0:
atom (3456):
atom[0,...,3455] = {28,...,3483}
weight: not available
pbcatom = 1755
Where 1755 = 1741+14 so again it looks as if the pull_pbcatom0 is
defined (or at least decided) in the context of the entire .gro file.
Now I reverse the order of the protein and the lipid, with only one
copy of the protein again.
Here, I specify pull_pbcatom0=10 (pull group 0 remains the lipid):
grompp says:
Pull group natoms pbc atom distance at start reference at t=0
0 345610
114 3463 -0.000 0.000 -0.001 0.000 0.000 0.000
and the .log file says:
pull_group 0:
atom (3456):
atom[0,...,3455] = {0,...,3455}
weight: not available
pbcatom = 9
Now I specify pull_pbcatom0=0
grompp says:
Pull group natoms pbc atom distance at start refe
[gmx-users] (no subject)
Hi I want to add acetyl group at the N and C terminal of my protein. i.e. CH3-C=O NH QQQ NH CH3 by removing the NH3+ and COO- at the N and C terminal. Please suggest what steps I have to follow. regards M. Baskar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
munu...@yahoo.com wrote: Hi I want to add acetyl group at the N and C terminal of my protein. i.e. CH3-C=O NH QQQ NH CH3 by removing the NH3+ and COO- at the N and C terminal. Please suggest what steps I have to follow. There are no programs in Gromacs that will do that. You may find some useful programs here: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin regards M. Baskar -- 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/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/mailing_lists/users.php
[gmx-users] Energy minimisation of solvated protein - Tutorial
Hi, I have the same problem as listed below back in February. I am using the latest gromacs version (4.0.7) and tried the solution below by entering genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of making the output as pdb file. Yet the same result occurs with the same error message. One of the box lengths is smaller than twice the cut-off length. Please let me know what other options I can try. Thanks! nayef -- original message below -- Hi Anna, You should mention the version of Gromacs you're using. One of the versions did not write the box correctly to pdb files, which I think happened in your case. If you take as the solvation step genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of writing output to 1qlz-water.pdb, I think you should be fine. The reason for writing a .pdb file is the easier visualization with a multitude of programs. Thanks for your interest in the tutorial. Cheers, Tsjerk On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan wrote: Hi, I've been trying to go through the 'Introduction to Molecular Dynamics Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the tutorials listed on the GROMACS website. I've got to the stage where I am performing energy minimisation on my solvated protein but when I use grompp to create the .tpr file for mdrun, I get the error message: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I am using the protein with pdb ID 1QLZ, one of the suggested structures for the tutorial and have so far carried out the following commands: % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname NA+ -nname CL- % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr after which I receive the error message. The minim_pbd.mdp file I use in the last grompp command is the same as minim.mdp used in previous grompp commands (the latter file I downloaded as part of the tutorial) except that the line 'pbc = no' has been replaced by 'pbc = xyz'. I have tried increasing the value of 'd' in the editconf command, to 2,3 and even 8 but this doesn't make any difference. (I have read that it is not a good idea to tamper with the cut-off values so have avoided doing that) The box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... Anna -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] building up a long polymer chain
Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues need atom numbering..Hdb file was not helpful either because I think I need to have a structure file with only coordinates of carbon atoms (hdb adds H ). ...That coordinate file I dont know how to get. I tried x2top command to generate top file and I got LINCS error. I followd the tips you had given before on how to diagnose a crashing system and thats why I suspect top file is not produced properly when I have no atom numbering in coordinate file. Now I am following your suggestion to use genconf command to build up my polymer. The distance between C -C atoms in ethylene is 1.52 A. So I considred 0.76 A as distance from each side, and 1.52+ 2*0.76=3.04 A as box size. In the command line below I entered 0.304 to convert to nm. Please see below: Initsial pdb file: HETATM1 C1 EthB1 2.739 2.554 -0.012 0.00 -0.39 C HETATM2 H11 EthB1 2.736 3.644 -0.012 0.00 0.13 H HETATM3 H12 EthB1 2.190 2.217 -0.893 0.00 0.13 H HETATM4 H13 EthB1 2.190 2.217 0.868 0.00 0.13 H HETATM5 C2 EthB1 4.155 1.993 -0.012 0.00 -0.26 C HETATM6 H21 EthB1 4.696 2.362 -0.887 0.00 0.13 H HETATM7 H22 EthB1 4.696 2.362 0.862 0.00 0.13 H END editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 0.304 0.304 -angles 90 90 90 -d 0.076 7 1EthBC11 0.141 0.166 0.164 1EthB H112 0.141 0.275 0.164 1EthB H123 0.086 0.132 0.076 1EthB H134 0.086 0.132 0.252 1EthBC25 0.282 0.110 0.164 1EthB H216 0.337 0.147 0.077 1EthB H227 0.337 0.147 0.251 0.40260 0.31710 0.32810 0.0 0.0 0.0 0.0 0.0 0.0 genconf -f PEmonomer.gro -sort -o PEsort -nbox 5 I use -sort to align the molecule with X coordinate and want to replicate 5 boxes. Am I using correctly the -sort option? What I get is: 8875 1EthBC11 0.086 0.132 0.252 0. 0. 0. 1EthB H112 0.282 0.110 0.164 0. 0. 0. 1EthB H123 0.337 0.147 0.077 0. 0. 0. 1EthB H134 0.086 0.132 0.404 0. 0. 0. 1EthBC25 0.086 0.132 0.580 0. 0. 0. 1EthB H216 0.282 0.110 0.492 0. 0. 0. 1EthB H227 0.086 0.132 1.236 0. 0. 0. 2EthBC18 0.282 0.110 1.148 0. 0. 0. 2EthB H119 0.337 0.147 1.061 0. 0. 0. 2EthB H12 10 0.086 0.132 1.388 0. 0. 0. 2EthB H13 11 0.086 0.132 1.564 0. 0. 0. 2EthBC2 12 0.282 0.110 1.476 0. 0. 0. 2EthB H21 13 0.086 0.449 0.580 0. 0. 0. 2EthB H22 14 0.282 0.427 0.492 0. 0. 0. 3EthBC1 15 0.337 0.464 0.405 0. 0. 0. 3EthB H11 16 0.086 0.449 0.732 0. 0. 0. To me what I have done is not right. 1- I am replicating CH3CH, while what I need is CH2CH2. Even when I do this I need to somehow add in CH3 to both ends! Please guide me on this issue 2- I am sure something is wrong. When I use -box 5 I get 8875 monomer units! Thank you, Moeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] building up a long polymer chain
Moeed wrote: Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues need atom numbering..Hdb file was not helpful either because I think I need to have a structure file with only coordinates of carbon atoms (hdb adds H ). ...That coordinate file I dont know how to get. http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources With both PRODRG and xLeap you should be able to easily build a short repeat unit. You will have to rename the constituent atoms, but at least the coordinate files are syntactically correct. I tried x2top command to generate top file and I got LINCS error. I followd the tips you had given before on how to diagnose a crashing system and thats why I suspect top file is not produced properly when I have no atom numbering in coordinate file. Now I am following your Well, I have never dealt with something like that, but if you're coordinate file is useless, then so too will the topology, likely. suggestion to use genconf command to build up my polymer. The distance between C -C atoms in ethylene is 1.52 A. So I considred 0.76 A as distance from each side, and 1.52+ 2*0.76=3.04 A as box size. In the command line below I entered 0.304 to convert to nm. Please see below: Initsial pdb file: HETATM1 C1 EthB1 2.739 2.554 -0.012 0.00 -0.39 C HETATM2 H11 EthB1 2.736 3.644 -0.012 0.00 0.13 H HETATM3 H12 EthB1 2.190 2.217 -0.893 0.00 0.13 H HETATM4 H13 EthB1 2.190 2.217 0.868 0.00 0.13 H HETATM5 C2 EthB1 4.155 1.993 -0.012 0.00 -0.26 C HETATM6 H21 EthB1 4.696 2.362 -0.887 0.00 0.13 H HETATM7 H22 EthB1 4.696 2.362 0.862 0.00 0.13 H END editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 0.304 0.304 -angles 90 90 90 -d 0.076 Going by the nomenclature of the system we've been discussing for the last eternity, EthB is a "beginning" residue, i.e. CH3-CH2-, when what you want to be using is Eth, which is a -CH2-CH2- unit. Once you've built the coordinate file, change the names of the beginning and end residues and process the structure with pdb2gmx to build back the right hydrogens. By specifying both -box and -d, you are adding extra space in the box. The use of -angles is not necessary, and somehow you are not getting a cubic box: 0.40260 0.31710 0.32810 0.0 0.0 0.0 0.0 0.0 0.0 The proper command for what you want is: editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 -bt cubic genconf -f PEmonomer.gro -sort -o PEsort -nbox 5 I use -sort to align the molecule with X coordinate and want to replicate 5 boxes. Am I using correctly the -sort option? What I get is: 8875 1EthBC11 0.086 0.132 0.252 0. 0. 0. 1EthB H112 0.282 0.110 0.164 0. 0. 0. 1EthB H123 0.337 0.147 0.077 0. 0. 0. 1EthB H134 0.086 0.132 0.404 0. 0. 0. 1EthBC25 0.086 0.132 0.580 0. 0. 0. 1EthB H216 0.282 0.110 0.492 0. 0. 0. 1EthB H227 0.086 0.132 1.236 0. 0. 0. 2EthBC18 0.282 0.110 1.148 0. 0. 0. 2EthB H119 0.337 0.147 1.061 0. 0. 0. 2EthB H12 10 0.086 0.132 1.388 0. 0. 0. 2EthB H13 11 0.086 0.132 1.564 0. 0. 0. 2EthBC2 12 0.282 0.110 1.476 0. 0. 0. 2EthB H21 13 0.086 0.449 0.580 0. 0. 0. 2EthB H22 14 0.282 0.427 0.492 0. 0. 0. 3EthBC1 15 0.337 0.464 0.405 0. 0. 0. 3EthB H11 16 0.086 0.449 0.732 0. 0. 0. To me what I have done is not right. 1- I am replicating CH3CH, while what I need is CH2CH2. Even when I do this I need to somehow add in CH3 to both ends! Please guide me on this issue See above. 2- I am sure something is wrong. When I use -box 5 I get 8875 monomer units! Yes, because when a GROMACS command expects a vector quantity, and receives only a scalar, it is applied uniformly in all directions. This is documented in the manual. I also see no purpose whatsoever to using -sort. What you need is: genconf -f PEmonomer.gro -o PEchain.gro -nbox 5 1 1 -Justin Thank you, Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 23
[gmx-users] g_dihfix program
Hi, I am reconstructing atomic details from coarse-grained MD structure using gromacs-reverse. I am following reverse transform tutorial at MARTINI Website and also this paper http://www3.interscience.wiley.com/cgi-bin/fulltext/123244279/HTMLSTART I am unable to find g_dihfix program to restrain dihedral angles and to modify my topology file to include dihedral_restraints. >From where I can get g_dihfix program. Thank you for the help. -- Vandana Kumari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] umbrella sampling-Bimodal Histograms
I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, wrote: > Please clarify: > > Are doing SMD or are you doing US? If you're doing SMD then you should not > be using WHAM and you should not really be able to generate any sampling > histograms. > > Are the histograms that you are referring to population densities of the > sampling along your reaction coordinate? > > My guess -- if you're doing US -- is that you have some incorrect pull > group settings. Bimodal distributions are indeed possible, but should > require very long sampling times to achieve, and I doubt that you are at > those times yet. Your Fc is fine. Post your pull settings. > > Chris. > > -- original message -- > > When i did the Umbrella sampling of frames from an SMD (of ligand > transport), I am getting bimodal histograms in some cases. > > Do you think this is because , the force constant that i used is very low > (i > used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my > PMF result? Do I need to repeat the sampling again with another pull_k1 > value(higher value)? > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] umbrella sampling-Bimodal Histograms
Take that replica on the left that shows a bimodal histogram. Now plot a time series of the displacement: x-axis = time and y-axis = displacement along reaction coord. Is it jumping back and forth between two regions of sampling? Probably not... more likely it starts near one maximum and transitions to another maximum. If this is true then it simply means that you have not equilibrated enough. Run longer and cut some of the initial sampling. Chris. -- original message -- I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, wrote: Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Energy minimisation of solvated protein - Tutorial
Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher wrote: > Hi, > > I have the same problem as listed below back in February. I am using the > latest gromacs version (4.0.7) and tried the solution below by entering > > genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro > > instead of making the output as pdb file. Yet the same result occurs with > the same error message. One of the box lengths is smaller than twice the > cut-off length. > > Please let me know what other options I can try. > > Thanks! > > nayef > -- > original message below > -- > > Hi Anna, > > You should mention the version of Gromacs you're using. One of the > versions did not write the box correctly to pdb files, which I think > happened in your case. If you take as the solvation step > > genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro > > instead of writing output to 1qlz-water.pdb, I think you should be fine. > > The reason for writing a .pdb file is the easier visualization with a > multitude of programs. > > Thanks for your interest in the tutorial. > > Cheers, > > Tsjerk > > On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan > wrote: >> >> Hi, >> >> I've been trying to go through the 'Introduction to Molecular Dynamics >> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the >> tutorials listed on the GROMACS website. >> >> I've got to the stage where I am performing energy minimisation on my >> solvated protein but when I use grompp to create the .tpr file for mdrun, >> I >> get the error message: >> >> One of the box lengths is smaller than twice the cut-off length. Increase >> the box size or decrease rlist >> >> >> I am using the protein with pdb ID 1QLZ, one of the suggested structures >> for >> the tutorial and have so far carried out the following commands: >> >> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh >> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr >> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb >> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 >> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb >> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr >> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname >> NA+ -nname CL- >> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o >> 1qlz-EM-solvated.tpr >> >> after which I receive the error message. >> >> The minim_pbd.mdp file I use in the last grompp command is the same as >> minim.mdp used in previous grompp commands (the latter file I downloaded >> as >> part of the tutorial) except that the line 'pbc = no' has been replaced by >> 'pbc = xyz'. >> >> I have tried increasing the value of 'd' in the editconf command, to 2,3 >> and >> even 8 but this doesn't make any difference. (I have read that it is not >> a >> good idea to tamper with the cut-off values so have avoided doing that) >> The >> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 >> in >> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... >> >> Anna >> -- >> gmx-users mailing list gmx-users at gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Energy minimisation of solvated protein - Tutorial
remember to change the pbc = xyz from pbc = no. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, June 22, 2010 12:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation of solvated protein - Tutorial Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher wrote: > Hi, > > I have the same problem as listed below back in February. I am using the > latest gromacs version (4.0.7) and tried the solution below by entering > > genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro > > instead of making the output as pdb file. Yet the same result occurs with > the same error message. One of the box lengths is smaller than twice the > cut-off length. > > Please let me know what other options I can try. > > Thanks! > > nayef > -- > original message below > -- > > Hi Anna, > > You should mention the version of Gromacs you're using. One of the > versions did not write the box correctly to pdb files, which I think > happened in your case. If you take as the solvation step > > genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro > > instead of writing output to 1qlz-water.pdb, I think you should be fine. > > The reason for writing a .pdb file is the easier visualization with a > multitude of programs. > > Thanks for your interest in the tutorial. > > Cheers, > > Tsjerk > > On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan > wrote: >> >> Hi, >> >> I've been trying to go through the 'Introduction to Molecular Dynamics >> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the >> tutorials listed on the GROMACS website. >> >> I've got to the stage where I am performing energy minimisation on my >> solvated protein but when I use grompp to create the .tpr file for mdrun, >> I >> get the error message: >> >> One of the box lengths is smaller than twice the cut-off length. Increase >> the box size or decrease rlist >> >> >> I am using the protein with pdb ID 1QLZ, one of the suggested structures >> for >> the tutorial and have so far carried out the following commands: >> >> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh >> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr >> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb >> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 >> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb >> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr >> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname >> NA+ -nname CL- >> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o >> 1qlz-EM-solvated.tpr >> >> after which I receive the error message. >> >> The minim_pbd.mdp file I use in the last grompp command is the same as >> minim.mdp used in previous grompp commands (the latter file I downloaded >> as >> part of the tutorial) except that the line 'pbc = no' has been replaced by >> 'pbc = xyz'. >> >> I have tried increasing the value of 'd' in the editconf command, to 2,3 >> and >> even 8 but this doesn't make any difference. (I have read that it is not >> a >> good idea to tamper with the cut-off values so have avoided doing that) >> The >> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 >> in >> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... >> >> Anna >> -- >> gmx-users mailing listgmx-users at gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to gmx-users-request at gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listg
Re: [gmx-users] Energy miscalculation
Hi Thanasis, Chris, I read the first while there was only one :p I agree that most people (including me) will not readily go through eight lengthy posts as an introduction to an issue. But the issue raised does seem in need of attention. Not mine though :p Also, the stream-of-consciousness approach both in sending mails as well as writing each is not the most convenient. Maybe you can write a summary that starts with what you're trying to do, what you'd expect, what you got that you didn't expect, and then the digging deeper and deeper (presented systematically) to help provide us with clues on the origin of the problem. Cheers, Tsjerk On Mon, Jun 21, 2010 at 4:38 PM, wrote: > Dear Thanasis: > > 8 posts on the same topic? I didn't even read them. If you want some help, > I'd suggest that you start with a new subject line and post a single email > containing all relevant information. > > You can see how it looks at the bottom of this list: > http://lists.gromacs.org/pipermail/gmx-users/2010-June/date.html > > And perhaps you can imagine that many of us are a little hesitant to read 8 > emails that may or may not be repeats of the same information. > > Chris. > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
