[gmx-users] MDRUN crash
Luca Banetta
luca.banetta at gmail.com
Fri Jun 17 13:52:07 CEST 2016
thank you for your great useful help justin! I have just written two
directives in which I declare polarization and exlusions as you wrote
me on the previous e-mail
[ polarization ]
; Vsite shell functiontype alpha nm^3
11 12 1 0.001
[ exclusions ]
;
4 1 2 3 5 6 7 8 9 10 11 12
11 1 2 3 4 5 6 7 8 9 10 12
The mdp file is the following one
;
; File 'mdout.mdp' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Fri Jun 17 13:45:51 2016
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.0001
nsteps = 1000000
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 100
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 50
nstcalcenergy = -1
nstenergy = 50
; Output frequency and precision for .xtc file
nstxtcout = 50
xtc-precision = 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 0.9
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; Optimization of QM subsystem
bOPT =
bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = no
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Dihedral angle restraints: No or Yes
dihre = No
dihre-fc = 1000
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
foreign_lambda =
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
nstdhdl = 10
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
But unfortunately immediately after I launch the mdrun this fatal error appears:
Fatal error:
1629 particles communicated to PME node 4 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
What can i do in order to fix it?
2016-06-17 12:03 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 6/17/16 3:56 AM, Luca Banetta wrote:
>>
>> Thank you for your support mark! I run an equilibration with a simple
>> acetone molecule and it works with the mdp file i wrote in the first
>> e-mail. I try to take a look at the shell to see if i made mistakes in its
>> definition.
>
>
> Yes, the topology is wrong if you're trying to use a polarizable model. You
> have a virtual particle (11) with a negative charge and (presumably) a shell
> particle with an equivalent charge, defined as being bonded to the virtual
> particle. But it's not actually a polarizable system (you need to define a
> [polarization] directive with the attributes of the shell, e.g. atomic
> polarizability) and you need to exclude the virtual site from the shell and
> the other atoms that the O atom is excluded from. Without doing this,
> you're just generating huge forces on everything due to electrostatic
> repulsion.
>
> -Justin
>
>
>> Il 17/Giu/2016 08:47, "Mark Abraham" <mark.j.abraham at gmail.com> ha
>> scritto:
>>
>>> Hi,
>>>
>>> Please don't start new work with old out-of-maintenance software, or at
>>> least use the most recent bug fix from that release branch. You should
>>> also
>>> do an equilibration with a normal acetone first, so that you know whether
>>> it's your equilibration or your shell model that is the problem.
>>>
>>> Mark
>>>
>>> On Fri, Jun 17, 2016 at 8:44 AM Luca Banetta <luca.banetta at gmail.com>
>>> wrote:
>>>
>>>> thank you for the advice justin! i have made some research and i use PME
>>>> for electrostatics that i noticed it's pretty common. Unfortunately the
>>>> mdrun this fatal error appeared:
>>>> Program mdrun, VERSION 4.5.4
>>>> Source code file: pme.c, line: 538
>>>>
>>>> Fatal error:
>>>> 1629 particles communicated to PME node 4 are more than 2/3 times the
>>>> cut-off out of the domain decomposition cell of their charge group in
>>>> dimension x.
>>>> This usually means that your system is not well equilibrated.
>>>>
>>>>
>>>> For out simulation we created a topology for the acetone molecule using
>>>> opls-AA force field introudicing a shell particle inside the topology.
>>>> At the moment the simulation is based on a single acetone molecule
>>>
>>> inside a
>>>>
>>>> "sea" of water.
>>>> [ moleculetype ]
>>>> ; Name nrexcl
>>>> acetone 3
>>>>
>>>> [ atoms ]
>>>> ; nr type resnr residue atom cgnr charge
>>>> mass typeB chargeB massB
>>>> 1 opls_280 1 LIG C 1 0.47
>>>> 12.011
>>>> 2 opls_135 1 LIG C 2 -0.18
>>>> 12.011
>>>> 3 opls_135 1 LIG C 3 -0.18
>>>> 12.011
>>>> 4 opls_281 1 LIG O 4 0.47
>>>> 15.5994
>>>> 5 opls_282 1 LIG H 5 0.06
>>>> 1.008
>>>> 6 opls_282 1 LIG H 6 0.06
>>>> 1.008
>>>> 7 opls_282 1 LIG H 7 0.06
>>>> 1.008
>>>> 8 opls_282 1 LIG H 8 0.06
>>>> 1.008
>>>> 9 opls_282 1 LIG H 9 0.06
>>>> 1.008
>>>> 10 opls_282 1 LIG H 10 0.06
>>>> 1.008
>>>> 11 VS 1 LIG VS 11
>>>> -0.47 0.000
>>>> 12 SP 1 LIG SP 12
>>>> -0.47 0.000
>>>>
>>>> [ bonds ]
>>>> ; ai aj funct c0 c1 c2
>>>> c3
>>>> 1 2 1
>>>> 1 3 1
>>>> 1 4 1
>>>> 4 11 6
>>>> 11 12 6
>>>> 2 5 1
>>>> 2 6 1
>>>> 2 7 1
>>>> 3 8 1
>>>> 3 9 1
>>>> 3 10 1
>>>>
>>>> [ pairs ]
>>>> ; ai aj funct c0 c1 c2
>>>> c3
>>>> 2 8 1
>>>> 2 9 1
>>>> 2 10 1
>>>> 3 5 1
>>>> 3 6 1
>>>> 3 7 1
>>>> 4 5 1
>>>> 4 6 1
>>>> 4 7 1
>>>> 4 8 1
>>>> 4 9 1
>>>> 4 10 1
>>>>
>>>> [ angles ]
>>>> ; ai aj ak funct c0 c1
>>>> c2 c3
>>>> 2 1 3 1
>>>> 2 1 4 1
>>>> 3 1 4 1
>>>> 1 2 5 1
>>>> 1 2 6 1
>>>> 1 2 7 1
>>>> 5 2 6 1
>>>> 5 2 7 1
>>>> 6 2 7 1
>>>> 1 3 8 1
>>>> 1 3 9 1
>>>> 1 3 10 1
>>>> 8 3 9 1
>>>> 8 3 10 1
>>>> 9 3 10 1
>>>>
>>>> [ dihedrals ]
>>>> ; ai aj ak al funct c0 c1
>>>> c2 c3 c4 c5
>>>> 3 1 2 5 3
>>>> 3 1 2 6 3
>>>> 3 1 2 7 3
>>>> 4 1 2 5 3
>>>> 4 1 2 6 3
>>>> 4 1 2 7 3
>>>> 2 1 3 8 3
>>>> 2 1 3 9 3
>>>> 2 1 3 10 3
>>>> 4 1 3 8 3
>>>> 4 1 3 9 3
>>>> 4 1 3 10 3
>>>>
>>>> [ virtual_sites2 ]
>>>> ; site ai aj funct a
>>>> 11 1 4 1 1.05
>>>>
>>>> VS and SP have been introduced in the "ffnonbonded" and "ffbonded"
>>>
>>> sections
>>>>
>>>> in the library oplsaa.ff
>>>>
>>>> 2016-06-16 15:05 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>>
>>>>>
>>>>> On 6/16/16 6:10 AM, Luca Banetta wrote:
>>>>>
>>>>>> Dear gmx users,
>>>>>> I am meeting a lot of problems launching a simulation with shell
>>>>>> particles.
>>>>>> The mdp file is
>>>>>> ; VARIOUS PREPROCESSING OPTIONS
>>>>>> title = Yo
>>>>>> cpp = /usr/bin/cpp
>>>>>> include =
>>>>>> define =
>>>>>>
>>>>>> ; RUN CONTROL PARAMETERS
>>>>>> integrator = md
>>>>>> ; Start time and timestep in ps
>>>>>> tinit = 0
>>>>>> dt = 0.001
>>>>>> nsteps = 1000000
>>>>>> ; For exact run continuation or redoing part of a run
>>>>>> init_step = 0
>>>>>> ; mode for center of mass motion removal
>>>>>> comm-mode = Linear
>>>>>> ; number of steps for center of mass motion removal
>>>>>> nstcomm = 1
>>>>>> ; group(s) for center of mass motion removal
>>>>>> comm-grps =
>>>>>>
>>>>>> ; LANGEVIN DYNAMICS OPTIONS
>>>>>> ; Temperature, friction coefficient (amu/ps) and random seed
>>>>>> bd-temp = 300
>>>>>> bd-fric = 0
>>>>>> ld-seed = 1993
>>>>>>
>>>>>> ; ENERGY MINIMIZATION OPTIONS
>>>>>> ; Force tolerance and initial step-size
>>>>>> emtol = 100
>>>>>> emstep = 0.01
>>>>>> ; Max number of iterations in relax_shells
>>>>>> niter = 20
>>>>>> ; Step size (1/ps^2) for minimization of flexible constraints
>>>>>> fcstep = 0
>>>>>> ; Frequency of steepest descents steps when doing CG
>>>>>> nstcgsteep = 1000
>>>>>> nbfgscorr = 10
>>>>>>
>>>>>> ; OUTPUT CONTROL OPTIONS
>>>>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>>>>> nstxout =
>>>>>> nstvout =
>>>>>> nstfout =
>>>>>> ; Checkpointing helps you continue after crashes
>>>>>> nstcheckpoint = 1000
>>>>>> ; Output frequency for energies to log file and energy file
>>>>>> nstlog = 50
>>>>>> nstenergy = 50
>>>>>> ; Output frequency and precision for xtc file
>>>>>> nstxtcout = 50
>>>>>> xtc-precision = 1000
>>>>>> ; This selects the subset of atoms for the xtc file. You can
>>>>>> ; select multiple groups. By default all atoms will be written.
>>>>>> xtc-grps =
>>>>>> ; Selection of energy groups
>>>>>> energygrps =
>>>>>>
>>>>>> ; NEIGHBORSEARCHING PARAMETERS
>>>>>> ; nblist update frequency
>>>>>> nstlist = 5
>>>>>> ; ns algorithm (simple or grid)
>>>>>> ns_type = grid
>>>>>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>>>>>> ; or full (infinite systems only)
>>>>>> pbc = xyz
>>>>>> ; nblist cut-off
>>>>>> rlist = 0.9
>>>>>> domain-decomposition = no
>>>>>>
>>>>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>>>>> ; Method for doing electrostatics
>>>>>> coulombtype = Cut-off
>>>>>> rcoulomb-switch = 0
>>>>>> rcoulomb = 0.9
>>>>>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>>>>>> epsilon-r = 1
>>>>>> ; Method for doing Van der Waals
>>>>>> vdw-type = Cut-off
>>>>>> ; cut-off lengths
>>>>>> rvdw-switch = 0
>>>>>> rvdw = 0.9
>>>>>> ; Apply long range dispersion corrections for Energy and Pressure
>>>>>> DispCorr = EnerPres
>>>>>> ; Extension of the potential lookup tables beyond the cut-off
>>>>>> table-extension = 1
>>>>>> ; Spacing for the PME/PPPM FFT grid
>>>>>> fourierspacing = 0.12
>>>>>> ; FFT grid size, when a value is 0 fourierspacing will be used
>>>>>> fourier_nx = 0
>>>>>> fourier_ny = 0
>>>>>> fourier_nz = 0
>>>>>> ; EWALD/PME/PPPM parameters
>>>>>> pme_order = 4
>>>>>> ewald_rtol = 1e-05
>>>>>> ewald_geometry = 3d
>>>>>> epsilon_surface = 0
>>>>>> optimize_fft = no
>>>>>>
>>>>>> ; GENERALIZED BORN ELECTROSTATICS
>>>>>> ; Algorithm for calculating Born radii
>>>>>> gb_algorithm = Still
>>>>>> ; Frequency of calculating the Born radii inside rlist
>>>>>> nstgbradii = 1
>>>>>> ; Cutoff for Born radii calculation; the contribution from atoms
>>>>>> ; between rlist and rgbradii is updated every nstlist steps
>>>>>> rgbradii = 2
>>>>>> ; Salt concentration in M for Generalized Born models
>>>>>> gb_saltconc = 0
>>>>>>
>>>>>> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
>>>>>> implicit_solvent = No
>>>>>>
>>>>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>>>>>> ; Temperature coupling
>>>>>> Tcoupl = berendsen
>>>>>> ; Groups to couple separately
>>>>>> tc-grps = System
>>>>>> ; Time constant (ps) and reference temperature (K)
>>>>>> tau_t = 0.1
>>>>>> ref_t = 300
>>>>>> ; Pressure coupling
>>>>>> Pcoupl = berendsen
>>>>>> Pcoupltype = isotropic
>>>>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>>>>>> tau_p = 1.0
>>>>>> compressibility = 4.5e-5
>>>>>> ref_p = 1.0
>>>>>> ; Random seed for Andersen thermostat
>>>>>> andersen_seed = 815131
>>>>>>
>>>>>> ; SIMULATED ANNEALING
>>>>>> ; Type of annealing for each temperature group (no/single/periodic)
>>>>>> annealing = no
>>>>>> ; Number of time points to use for specifying annealing in each group
>>>>>> annealing_npoints =
>>>>>> ; List of times at the annealing points for each group
>>>>>> annealing_time =
>>>>>> ; Temp. at each annealing point, for each group.
>>>>>> annealing_temp =
>>>>>>
>>>>>> ; GENERATE VELOCITIES FOR STARTUP RUN
>>>>>> gen_vel = yes
>>>>>> gen_temp = 300
>>>>>> gen_seed = 1993
>>>>>>
>>>>>> ; OPTIONS FOR BONDS
>>>>>> constraints = all-bonds
>>>>>> ; Type of constraint algorithm
>>>>>> constraint-algorithm = Lincs
>>>>>> ; Do not constrain the start configuration
>>>>>> unconstrained-start = no
>>>>>> ; Use successive overrelaxation to reduce the number of shake
>>>
>>> iterations
>>>>>>
>>>>>> Shake-SOR = no
>>>>>> ; Relative tolerance of shake
>>>>>> shake-tol = 1e-04
>>>>>> ; Highest order in the expansion of the constraint coupling matrix
>>>>>> lincs-order = 4
>>>>>> ; Number of iterations in the final step of LINCS. 1 is fine for
>>>>>> ; normal simulations, but use 2 to conserve energy in NVE runs.
>>>>>> ; For energy minimization with constraints it should be 4 to 8.
>>>>>> lincs-iter = 1
>>>>>> ; Lincs will write a warning to the stderr if in one step a bond
>>>>>> ; rotates over more degrees than
>>>>>> lincs-warnangle = 30
>>>>>> ; Convert harmonic bonds to morse potentials
>>>>>> morse = no
>>>>>>
>>>>>> ; ENERGY GROUP EXCLUSIONS
>>>>>> ; Pairs of energy groups for which all non-bonded interactions are
>>>>>> excluded
>>>>>> energygrp_excl =
>>>>>>
>>>>>> ; NMR refinement stuff
>>>>>> ; Distance restraints type: No, Simple or Ensemble
>>>>>> disre = No
>>>>>> ; Force weighting of pairs in one distance restraint: Conservative or
>>>>>> Equal
>>>>>> disre-weighting = Conservative
>>>>>> ; Use sqrt of the time averaged times the instantaneous violation
>>>>>> disre-mixed = no
>>>>>> disre-fc = 1000
>>>>>> disre-tau = 0
>>>>>> ; Output frequency for pair distances to energy file
>>>>>> nstdisreout = 100
>>>>>> ; Orientation restraints: No or Yes
>>>>>> orire = no
>>>>>> ; Orientation restraints force constant and tau for time averaging
>>>>>> orire-fc = 0
>>>>>> orire-tau = 0
>>>>>> orire-fitgrp =
>>>>>> ; Output frequency for trace(SD) to energy file
>>>>>> nstorireout = 100
>>>>>> ; Dihedral angle restraints: No, Simple or Ensemble
>>>>>> dihre = No
>>>>>> dihre-fc = 1000
>>>>>> dihre-tau = 0
>>>>>> ; Output frequency for dihedral values to energy file
>>>>>> nstdihreout = 100
>>>>>>
>>>>>> ; Free energy control stuff
>>>>>> free-energy = no
>>>>>> init-lambda = 0
>>>>>> delta-lambda = 0
>>>>>> sc-alpha = 0
>>>>>> sc-sigma = 0.3
>>>>>>
>>>>>> ; Non-equilibrium MD stuff
>>>>>> acc-grps =
>>>>>> accelerate =
>>>>>> freezegrps =
>>>>>> freezedim =
>>>>>> cos-acceleration = 0
>>>>>>
>>>>>> ; Electric fields
>>>>>> ; Format is number of terms (int) and for all terms an amplitude
>>>
>>> (real)
>>>>>>
>>>>>> ; and a phase angle (real)
>>>>>> E-x =
>>>>>> E-xt =
>>>>>> E-y =
>>>>>> E-yt =
>>>>>> E-z =
>>>>>> E-zt =
>>>>>>
>>>>>> ; User defined thingies
>>>>>> user1-grps =
>>>>>> user2-grps =
>>>>>> userint1 = 0
>>>>>> userint2 = 0
>>>>>> userint3 = 0
>>>>>> userint4 = 0
>>>>>> userreal1 = 0
>>>>>> userreal2 = 0
>>>>>> userreal3 = 0
>>>>>> userreal4 = 0
>>>>>>
>>>>>>
>>>>>> In the log file it is written that RMS force on the shell is -nan and
>>>>
>>>> it
>>>>>>
>>>>>> can't do EM.
>>>>>> Can someone give me some advice in order to make EM possible?
>>>>>>
>>>>>
>>>>> Please provide full details about what the system is and how you built
>>>>> it. Also note that using plain cutoff electrostatics went out of style
>>>>> about 20 years ago as it is horribly inaccurate.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
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>>>>
>>> --
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>>>
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
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