On 4/26/12 11:00 AM, Yongchul Chung 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.
It does not make sense to calculate pressure during EM, so Gromacs outputs it as
zero. Since there are no velocities, any reported pressure value would be
meaningless.
-Justin
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
--
========================================
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
========================================
--
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