[gmx-users] Re: double precision energy minimization show zero pressure in gromacs 4.5.5
Yongchul Chung
yxc169 at case.edu
Fri Apr 27 16:38:00 CEST 2012
Can anyone from development comment on this? I see that now 4.6 is coming
out ... if this is a bug in the code, it would be nice if it's fixed in 4.6.
Greg
On Thu, Apr 26, 2012 at 11:00 AM, Yongchul Chung <yxc169 at case.edu> wrote:
> 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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