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Note while doing energy minimization
- anuvc84
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11 years 2 months ago #1387
by anuvc84
Note while doing energy minimization was created by anuvc84
Dear users,
while I am running grompp for Energy minimization of an octamer in a Polarizable water box using martini_v2.2P force field (ran using gromacs 4.5.3), i got the following note
NOTE 1 : The sum of the two largest charge group radii (0.280421) is larger than rlist (1.400000) - rcoulomb (1.200000) mdp file used is as follows: integrator = steep tinit = 0.0 dt = 0.02 nsteps = 5000 nstcomm = 1 comm-grps = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 1000 nstenergy = 100 nstxtcout = 1000 xtc_precision = 100 xtc-grps = energygrps = Protein PW nstlist = 5 ns_type = grid pbc = xyz rlist = 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 2.5 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = Berendsen tc-grps = Protein PW tau_t = 1.0 1.0 ref_t = 300 300 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 3e-4 3e-4 ref_p = 1.0 1.0 gen_vel = no gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 --------------------------------------- I tried changing rlist to 1.5, grompp ran with out any note or warning,but energy minimization finished with the message Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em-MtC-oct-min.gro to ./#em-MtC-oct-min.gro.2# Steepest Descents converged to machine precision in 448 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.6421524e+06 Maximum force = 3.1892145e+04 on atom 57482 Norm of force = 1.2798799e+02 The atom 57482 is from a water Can you please suggest me on how to overcome this warning? Thank you, with regards Anu[file martini_v2.P_example.mdp]:
The sum of the two largest charge group radii (0.280421) is larger than
rlist (1.400000) - rcoulomb (1.200000)
mdp file used is as follows:
integrator = steep
tinit = 0.0
dt = 0.02
nsteps = 5000
nstcomm = 1
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = Protein PW
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 2.5
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein PW
tau_t = 1.0 1.0
ref_t = 300 300
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
I tried changing rlist to 1.5, grompp ran with out any note or warning,but energy minimization finished with the message
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up em-MtC-oct-min.gro to ./#em-MtC-oct-min.gro.2#
Steepest Descents converged to machine precision in 448 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.6421524e+06
Maximum force = 3.1892145e+04 on atom 57482
Norm of force = 1.2798799e+02
The atom 57482 is from a water
Can you please suggest me on how to overcome this warning?
Thank you,
with regards
Anu
while I am running grompp for Energy minimization of an octamer in a Polarizable water box using martini_v2.2P force field (ran using gromacs 4.5.3), i got the following note
NOTE 1 : The sum of the two largest charge group radii (0.280421) is larger than rlist (1.400000) - rcoulomb (1.200000) mdp file used is as follows: integrator = steep tinit = 0.0 dt = 0.02 nsteps = 5000 nstcomm = 1 comm-grps = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 1000 nstenergy = 100 nstxtcout = 1000 xtc_precision = 100 xtc-grps = energygrps = Protein PW nstlist = 5 ns_type = grid pbc = xyz rlist = 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 2.5 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = Berendsen tc-grps = Protein PW tau_t = 1.0 1.0 ref_t = 300 300 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 3e-4 3e-4 ref_p = 1.0 1.0 gen_vel = no gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 --------------------------------------- I tried changing rlist to 1.5, grompp ran with out any note or warning,but energy minimization finished with the message Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em-MtC-oct-min.gro to ./#em-MtC-oct-min.gro.2# Steepest Descents converged to machine precision in 448 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.6421524e+06 Maximum force = 3.1892145e+04 on atom 57482 Norm of force = 1.2798799e+02 The atom 57482 is from a water Can you please suggest me on how to overcome this warning? Thank you, with regards Anu[file martini_v2.P_example.mdp]:
The sum of the two largest charge group radii (0.280421) is larger than
rlist (1.400000) - rcoulomb (1.200000)
mdp file used is as follows:
integrator = steep
tinit = 0.0
dt = 0.02
nsteps = 5000
nstcomm = 1
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = Protein PW
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 2.5
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein PW
tau_t = 1.0 1.0
ref_t = 300 300
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
I tried changing rlist to 1.5, grompp ran with out any note or warning,but energy minimization finished with the message
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up em-MtC-oct-min.gro to ./#em-MtC-oct-min.gro.2#
Steepest Descents converged to machine precision in 448 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.6421524e+06
Maximum force = 3.1892145e+04 on atom 57482
Norm of force = 1.2798799e+02
The atom 57482 is from a water
Can you please suggest me on how to overcome this warning?
Thank you,
with regards
Anu
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- djurre
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11 years 2 months ago #1388
by djurre
Replied by djurre on topic Note while doing energy minimization
It is a note, not a warning. It might give slightly worse energy conservation, however in my opinion this is minimal.
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