[gmx-users] MDRUN crash
Justin Lemkul
jalemkul at vt.edu
Fri Jun 17 13:55:45 CEST 2016
On 6/17/16 7:52 AM, Luca Banetta wrote:
> 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
>
This is not correct. The virtual site and shell have the same exclusions as the
parent atom. They shouldn't be excluded from every atom.
> 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?
>
You can't run a polarizable simulation with DD with any released version of the
code. So that's probably what's happening; it's been declared as a fatal error
in newer versions (I have it working in my Drude developmental repo, but let's
not go there until we know your approach is sound). Run either on one core (to
test) or via OpenMP only.
-Justin
> 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
>>>>>
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>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>
>> --
>> ==================================================
>>
>> 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.
--
==================================================
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
==================================================
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