[gmx-users] Error during NVT equillibration with nvt.log file
ram bio
rmbio861 at gmail.com
Fri Oct 16 18:19:52 CEST 2009
Dear Justin,
Thanks and I tried your suggestion, that is minimizing the system
without restraints and increasing the Fmax to 1000, the mdp file used
is as follows:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
and the ouput is :
Steepest Descents converged to Fmax < 1000 in 1192 steps
Potential Energy = -4.5402134e+05
Maximum force = 9.6024463e+02 on atom 3573
Norm of force = 3.8811920e+01
Later is used this as input for the NVT equillibration with the
following nvt.mdp file:
title = NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 323 323 323 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 323 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DPPC SOL_CL-
and the ouput nvt.log file is as under:
Input Parameters:
integrator = md
nsteps = 50000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 48
nky = 48
nkz = 60
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p = 1
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 = 815131
rlist = 1.2
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
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 = EnerPres
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 = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
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: 6048.01 12219 45018
ref_t: 323 323 323
tau_t: 0.1 0.1 0.1
anneal: No No No
ann_npoints: 0 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
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: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: 0.000
Generated table with 1100 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 7497 molecules.
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Removing pbc first time
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 9045
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: Protein_DPPC
1: SOL_CL-
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 31609 Atoms
Max number of connections per atom is 28
Total number of connections is 138849
Max number of graph edges per atom is 4
Total number of graph edges is 48078
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.83e-04
Initial temperature: 333.793 K
Started mdrun on node 0 Sun Jul 5 18:04:45 2009
Step Time Lambda
0 0.00000 0.00000
Grid: 10 x 10 x 13 cells
Long Range LJ corr.: <C6> 9.7327e-04
Long Range LJ corr.: Epot -2200.19, Pres: -136.406, Vir: 2200.19
Energies (kJ/mol)
Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
1.19670e+04 8.38636e+03 8.15057e+03 4.20390e+03 3.08430e+03
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.45274e+03 5.37063e+04 3.47509e+06 -2.20019e+03 -4.22052e+05
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-1.63954e+05 1.03877e+01 2.98084e+06 5.03020e+09 5.03318e+09
Conserved En. Temperature Pressure (bar) Cons. rmsd ()
5.03318e+09 1.91196e+07 1.03974e+08 9.31478e+00
and if i remove the the constraints and lowering the time step using
the following nvt.mdp file it is running:
title = NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 100000 ; 1 * 100000 = 100 ps
dt = 0.001 ; 1 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 323 323 323 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 323 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DPPC SOL_CL-
please suggest me is it ok to remove the constraints and run the NVT
equillibration.
Thanks
Ram
On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Gromacs users,
>>
>> I am doing protein in lipid-bilayer simulation and i am following the
>> procedure as per justin tutorial. I am able to insert the protein in
>> lipid bilayer and minimize the system as per Inflategro
>> procedure,during the total procedure the system was minimized in every
>> step.Then, I solvated and ionized sytem and minimized using the
>> following mdp file:
>>
>> ; minim.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> define = -DSTRONG_POSRES
>> integrator = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol = 500.0 ; Stop minimization when the maximum
>> force < 1000.0 kJ/mol/nm
>> emstep = 0.01 ; Energy step size
>> nsteps = 50000 ; Maximum number of (minimization)
>> steps to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how
>> to calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor
>> list and long range forces
>> ns_type = grid ; Method to determine neighbor list
>> (simple, grid)
>> rlist = 1.2 ; Cut-off for making neighbor list
>> (short range forces)
>> coulombtype = PME ; Treatment of long range
>> electrostatic interactions
>> rcoulomb = 1.2 ; Short-range electrostatic cut-off
>> rvdw = 1.2 ; Short-range Van der Waals cut-off
>> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>>
>> the output was as follows:
>>
>> Steepest Descents converged to Fmax < 500 in 4770 steps
>> Potential Energy = -3.8820288e+05
>> Maximum force = 4.4803549e+02 on atom 3573
>> Norm of force = 1.7854408e+01
>>
>> As the potential energy and Fmax values were agreeable , I proceeded
>> to equillibrate the system using NVT.
>>
>
> Did you minimize the structure without restraints, prior to NVT?
>
> <snip>
>
>> Angle G96Angle Proper Dih. Ryckaert-Bell. Improper Dih.
>> 2.20077e+04 8.54042e+03 6.78950e+03 4.34650e+03 3.03266e+03
>> LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
>> 4.76527e+03 5.50236e+04 8.36617e+06 -2.20019e+03 -4.46844e+05
>> Coul. recip. Position Rest. Potential Kinetic En. Total Energy
>> -1.65524e+05 1.07769e+01 7.85612e+06 5.88813e+10 5.88892e+10
>> Conserved En. Temperature Pressure (bar) Cons. rmsd ()
>> 5.88892e+10 2.23805e+08 1.21713e+09 3.10245e+01
>>
>
> In my experience, the combination of an astronomically high temperature and
> a repulsive temperature is indicative of restraining an unrestrainable
> starting structure. Try the EM I suggested above. Other than that, as I've
> suggested before, see the Advanced Troubleshooting page I created in the
> tutorial.
>
> -Justin
>
>> Please help me to proceed further and let me know where are the
>> mistakes lying and how to overcome them.
>>
>> Thanks in advance,
>>
>> Ram
>> _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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