[gmx-users] Error in MD simulation

[teklebrh at ualberta.ca]

Dear Gromacs users,

First I have to mention few points. I read all the LINCS error and  
tried a number of options.

1, Minimized well the system. and the Epot and Max Forces are very resonable.

Steepest Descents converged to Fmax < 100 in 379 steps
Potential Energy  = -1.0573750e+05
Maximum force     =  8.0876366e+01 on atom 1117
Norm of force     =  8.7360611e+00

2, Equlibrate well the system. It works for 100ps

Once I run NPT simulation using the following .mdp parameter set it  
shows the following error.

; The etire lines starting with ';' ARE COMMENTS

title		= NPT equilibration using the berendsen thermostat and  
barostat	; Title of run
cpp             = /usr/bin/cpp ; location of cpp on linux

; The following lines tell the program the standard locations where to  
find certain files

; 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

; RUN CONTROL PARAMETERS

integrator               = md ; leap-frog integrator
; Start time and timestep in ns
tinit                    = 0
dt                       = 0.002     ; 2fs
nsteps                   = 500000   ; 2*500 = 1ns

; THOSE OPTIONS REMOVE MOTION OF THE ASPHALTENE MODEL COMPUNDS  
RELATIVE TO THE SOLVENT/IONS

; 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                = System

; 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                    = 200
emstep                   = 0.01

; 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                  = 2000
nstvout                  = 2000
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file
nstxtcout                = 1000
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                 = BIS  HEP
; Selection of energy groups
energygrps               = BIS  HEP

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency
nstlist                  = 5
; ns algorithm (simple or grid)
ns-type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
; nblist cut-off
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics
coulombtype              = PME
rcoulomb                 = 1.2


; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw                     = 1.2

; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres ; account for the cut-off vdw scheme

; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.16

; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling is on
tcoupl                   = V-rescale; modified berendsen thermostat
; Groups to couple separately
tc-grps                  = BIS  HEP ; three coupling gropus
; Time constant (ps) and reference temperature (K)
tau-t                    = 0.1  0.1   ; time constant
ref-t                    = 298  298   ; reference temprature
; Pressure coupling is on
Pcoupl                   = berendsen; Pressure coupling is on
Pcoupltype               = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 3  3
compressibility          = 1.47e-4  1.47e-4  ; isothermal  
compressibility, bar^-1
ref-p                    = 1  1
; Random seed for Andersen thermostat
andersen_seed            = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = yes ; assign velocities from Maxwell  
distribution (MXD)
gen-temp                 = 298 ; temperature for MXD
gen-seed                 = 173529    ; used to initialize random  
generator for random velocities

; OPTIONS FOR BONDS
constraints              = all-bonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
; 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               = 2
; 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

==========

It run the simulation for quite sometime but it gives me an error of  
LINCS some how in the middle.

I try changing some parameter sets like step size,tau-p , tau-t,  
lincs-warnangle but did not overcame the problem.

Step 197685, LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000000, max 0.000001 (between atoms 1856 and 15982)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     97     98   35.3    0.1000   0.1000      0.1000

can some one give me an advice or help?

For my other 10 MD set up it works fine but with diffrent solvents.

rob