[gmx-users] Enc: 1-4 ineractions in double precision

Jessé Nóbrega jesseazevedo at yahoo.com.br
Sat Dec 19 13:46:11 CET 2009


Hi justin;


I'm grateful for your help, but unfortunately I didn't solve the problem. I made a change in my mdp file. This is my mdout.mdp:

==============================================================================================================
;
;    File 'mdout.mdp' was generated
;    By user: jesse (1001)
;    On host: slayer
;    At date: Fri Dec 18 16:14:29 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include                  = 
; e.g.: -DI_Want_Cookies -DMe_Too
define                   = 

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 1000000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part          = 1
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
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld-seed                  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 10
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                  = 500
nstvout                  = 500
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstenergy                = 100
; Output frequency and precision for xtc file
nstxtcout                = 0
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               = Protein Non-Protein

; 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

; 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                     = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 3.400
; 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-5
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes

; 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
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension       = 2.092

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl                   = v-rescale
; Groups to couple separately
tc-grps                  = Protein Non-Protein
; Time constant (ps) and reference temperature (K)
tau-t                    = 0.1 0.1
ref-t                    = 310 310
; Pressure coupling     
Pcoupl                   = berendsen
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 4  4
compressibility          = 4.5e-5  4.5e-5
ref-p                    = 1.0 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                = 
; 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                 = 300.0
gen_seed                 = 173529

; OPTIONS FOR BONDS    
constraints              = hbonds
; 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                = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 10
; 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
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0.3
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

=========================================================================================================================

When running mdrun, received the following warnings:

=========================================================================================================================

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 721 and 722)
bonds that rotated more than 30 degrees:    
 atom 1 atom 2  angle  previous, current, constraint length
    721    722   90.0    0.1000      inf      0.1000       
    721    723   90.0    0.1000      inf      0.1000       
    721    724   90.0    0.1000      inf      0.1000       
 ...
Warning: 1-4 interaction between 4359 and 4364 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 1195 and 1200 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 4625 and 4630 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 510 and 513 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 4494 and 4499 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 1382 and 1387 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 1061 and 1064 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 4398 and 4403 at distance inf which is larger than the 1-4 table size 4.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
rank 5 in job 1  slayer_35381   caused collective abort of all ranks
  exit status of rank 5: killed by signal 9
rank 3 in job 1  slayer_35381   caused collective abort of all ranks
  exit status of rank 3: killed by signal 9

================================================================================================================================================================================

Please, if it will not disturb you, could you help me how to solve this problem?



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