Hi all, I am carrying out energy minimization on bulk polymer system (N~20000) with integrator = l-bfgs in double precision gromacs 4.5.5. I am using tabulated force-fields for bonded, and non-bonded interactions. In the force field, the coulombic interaction is set to zero, hence, the output is zero in md.log file.
I used g_energy to check the energy and pressure of the system after the minimization is finished. For some reason, the pressure output for the system is 0 with gromacs 4.5.5. So I went back and checked the md.log file to see if this happens during the simulation or not, and I found at time = 0, the pressure is 0. I wanted to make sure that this has to do with gromacs version, and not how the mdp file is configured, so I did same minimization with gromacs 4.0.7. When using version 4.0.7 with the same input files, I get the pressure output just fine. The potential energy at the end of simulation for both cases are exactly the same (only difference is 4.0.7 converges at 1754 steps, and 4.5.5 converges at 2148 steps) It is possible that I am doing (or setting) something wrong since I'm using the same mdp file from 4.0.7 to 4.5.5. To check if I'm setting something wrong by default, I compared the md.log output between these two versions. It seems like there are a few new things with gromacs 4.5.5 that is missing in 4.0.7. For example, with 4.5.5 nstcalcenergy = -1 nstcouple = -1 nstpcouple = -1 rlistlong = 1.1 I see nstcalcenergy is the frequency of energy output during calculation so it does not affect any calculation. Also since I am not coupling my system to thermal/pressure bath, nstcouple, nspcouple, and rlistlong does not mean much here. So I suppose I can repeat the calculation again with 4.0.7 instead. But since I've already carried out lots of calculation with 4.5.5, I kind of do not want to repeat the steps again in calculating pressure values, if possible. If someone can help me with this, it would be great. I am appending snippet of md.log output from 4.5.5 and 4.0.7 below as a reference. Greg ### md.log file 4.5.5 ### :-) /nfs/01/cwr0351/GMX4.5.5/bin/mdrun_d (double precision) (-: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = l-bfgs nsteps = 100000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 100 comm_mode = Linear nstlog = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstcalcenergy = -1 nstenergy = 1 nstxtcout = 10 init_t = 0 delta_t = 0.003 xtcprec = 1000 nkx = 0 nky = 0 nkz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = TRUE bShakeSOR = FALSE etc = No nsttcouple = -1 epc = No epctype = Isotropic nstpcouple = -1 tau_p = 5 ref_p (3x3): ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord_scaling = No posres_com (3): posres_com[0]= 0.00000e+00 posres_com[1]= 0.00000e+00 posres_com[2]= 0.00000e+00 posres_comB (3): posres_comB[0]= 0.00000e+00 posres_comB[1]= 0.00000e+00 posres_comB[2]= 0.00000e+00 andersen_seed = -1 rlist = 1.1 rlistlong = 1.1 rtpi = 0.05 coulombtype = User rcoulomb_switch = 0 rcoulomb = 1 vdwtype = User rvdw_switch = 0 rvdw = 1 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 DispCorr = No free_energy = no init_lambda = 0 delta_lambda = 0 n_foreign_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 sc_sigma_min = 0.3 nstdhdl = 10 separate_dhdl_file = yes dhdl_derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 nwall = 0 wall_type = 9-3 wall_atomtype[0] = -1 wall_atomtype[1] = -1 wall_density[0] = 0 wall_density[1] = 0 wall_ewald_zfac = 3 pull = no disre = No disre_weighting = Conservative disre_mixed = FALSE dr_fc = 1000 dr_tau = 0 nstdisreout = 100 orires_fc = 0 orires_tau = 0 nstorireout = 100 dihre-fc = 1000 em_stepsize = 0.01 em_tol = 1e-10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000000 nbfgscorr = 10 ConstAlg = Lincs shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 lincs_iter = 1 bd_fric = 0 ld_seed = 1993 cos_accel = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 57597 ref_t: 0 tau_t: 0 anneal: No ann_npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp_flags[ 0]: 2 2 energygrp_flags[ 1]: 2 2 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Cut-off's: NS: 1.1 Coulomb: 1 LJ: 1 System total charge: 0.000 Read user tables from table_A_A.xvg with 501 data points. Tabscale = 50 points/nm Read user tables from table_A_B.xvg with 501 data points. Tabscale = 50 points/nm Read user tables from table_B_B.xvg with 501 data points. Tabscale = 50 points/nm Read user tables from table_b0.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b1.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b5.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b12.xvg with 2496 data points. Tabscale = 500 points/nm Read user tables from table_b17.xvg with 2496 data points. Tabscale = 500 points/nm Read user tables from table_b19.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b40.xvg with 2496 data points. Tabscale = 500 points/nm Read user tables from table_a1.xvg with 901 data points. Read user tables from table_a2.xvg with 901 data points. Read user tables from table_a3.xvg with 901 data points. Read user tables from table_a4.xvg with 181 data points. Read user tables from table_a5.xvg with 181 data points. Read user tables from table_d6.xvg with 181 data points. Read user tables from table_d7.xvg with 181 data points. Read user tables from table_d8.xvg with 181 data points. Read user tables from table_d9.xvg with 181 data points. Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. Initiating Low-Memory BFGS Minimizer Max number of connections per atom is 14 Total number of connections is 267000 Max number of graph edges per atom is 2 Total number of graph edges is 38300 Started Low-Memory BFGS Minimizer on node 0 Tue Apr 24 17:03:47 2012 Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e-10 Number of steps = 100000 Grid: 12 x 12 x 12 cells Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Tab. Bonds Tab. Bonds NC Tab. Angles Tab. Dih. LJ (SR) 4.13987e+03 3.14441e+04 2.31911e+04 3.37997e+04 -1.62435e+05 Coulomb (SR) Potential Pressure (bar) 0.00000e+00 -6.98604e+04 0.00000e+00 Using 10 BFGS correction steps. F-max = 2.17837e-01 on atom 15319 F-Norm = 3.37657e-02 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Tab. Bonds Tab. Bonds NC Tab. Angles Tab. Dih. LJ (SR) 4.13987e+03 3.14441e+04 2.31911e+04 3.37997e+04 -1.62435e+05 Coulomb (SR) Potential Pressure (bar) 0.00000e+00 -6.98604e+04 0.00000e+00 ### md.log for 4.0.7 ### :-) /nfs/01/cwr0351/local_GMX4.0.7_d/bin/mdrun_d_mpi (double precision) (-: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = l-bfgs nsteps = 100000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 100 comm_mode = Linear nstlog = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstenergy = 1 nstxtcout = 10 init_t = 0 delta_t = 0.003 xtcprec = 1000 nkx = 0 nky = 0 nkz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = TRUE bShakeSOR = FALSE etc = No epc = No epctype = Isotropic tau_p = 5 ref_p (3x3): ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord_scaling = No posres_com (3): posres_com[0]= 0.00000e+00 posres_com[1]= 0.00000e+00 posres_com[2]= 0.00000e+00 posres_comB (3): posres_comB[0]= 0.00000e+00 posres_comB[1]= 0.00000e+00 posres_comB[2]= 0.00000e+00 andersen_seed = -1 rlist = 1.1 rtpi = 0.05 coulombtype = User rcoulomb_switch = 0 rcoulomb = 1 vdwtype = User rvdw_switch = 0 rvdw = 1 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = No free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 nwall = 0 wall_type = 9-3 wall_atomtype[0] = -1 wall_atomtype[1] = -1 wall_density[0] = 0 wall_density[1] = 0 wall_ewald_zfac = 3 pull = no disre = No disre_weighting = Conservative disre_mixed = FALSE dr_fc = 1000 dr_tau = 0 nstdisreout = 100 orires_fc = 0 orires_tau = 0 nstorireout = 100 dihre-fc = 1000 em_stepsize = 0.01 em_tol = 1e-10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000000 nbfgscorr = 10 ConstAlg = Lincs shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 lincs_iter = 1 bd_fric = 0 ld_seed = 1993 cos_accel = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 57597 ref_t: 0 tau_t: 0 anneal: No ann_npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp_flags[ 0]: 2 2 energygrp_flags[ 1]: 2 2 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Cut-off's: NS: 1.1 Coulomb: 0 LJ: 1 System total charge: 0.000 Read user tables from table_A_A.xvg with 501 data points. Tabscale = 50 points/nm Read user tables from table_A_B.xvg with 501 data points. Tabscale = 50 points/nm Read user tables from table_B_B.xvg with 501 data points. Tabscale = 50 points/nm Read user tables from table_b0.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b1.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b5.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b12.xvg with 2496 data points. Tabscale = 500 points/nm Read user tables from table_b17.xvg with 2496 data points. Tabscale = 500 points/nm Read user tables from table_b19.xvg with 2501 data points. Tabscale = 500 points/nm Read user tables from table_b40.xvg with 2496 data points. Tabscale = 500 points/nm Read user tables from table_a1.xvg with 901 data points. Read user tables from table_a2.xvg with 901 data points. Read user tables from table_a3.xvg with 901 data points. Read user tables from table_a4.xvg with 181 data points. Read user tables from table_a5.xvg with 181 data points. Read user tables from table_d6.xvg with 181 data points. Read user tables from table_d7.xvg with 181 data points. Read user tables from table_d8.xvg with 181 data points. Read user tables from table_d9.xvg with 181 data points. Configuring nonbonded kernels... Testing x86_64 SSE2 support... present. Initiating Low-Memory BFGS Minimizer Max number of connections per atom is 11 Total number of connections is 209800 Max number of graph edges per atom is 2 Total number of graph edges is 38300 Started Low-Memory BFGS Minimization on node 0 Thu Apr 26 10:10:05 2012 Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e-10 Number of steps = 100000 Grid: 12 x 12 x 12 cells Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Tab. Bonds Tab. Bonds NC Tab. Angles Tab. Dih. LJ (SR) 4.13987e+03 3.14441e+04 2.31911e+04 3.37997e+04 -1.62435e+05 Coulomb (SR) Potential Pressure (bar) 0.00000e+00 -6.98604e+04 -5.12822e+02 Using 10 BFGS correction steps. F-max = 2.17837e-01 on atom 15319 F-Norm = 3.37657e-02 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Tab. Bonds Tab. Bonds NC Tab. Angles Tab. Dih. LJ (SR) 4.13987e+03 3.14441e+04 2.31911e+04 3.37997e+04 -1.62435e+05 Coulomb (SR) Potential Pressure (bar) 0.00000e+00 -6.98604e+04 -5.12824e+02
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