[gmx-users] Martini in Gromacs

[Neha Gandhi]

Hello,

I am trying to run coarse grained MD in gromacs. I get following errors,
should I reduce the time step? Your feedback is appreciated.


NOTE 1 [file prod1.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 2 [file prod1.mdp]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.


WARNING 1 [file prod1.mdp]:
  For proper integration of the Parrinello-Rahman barostat, tau-p (2)
  should be at least 20 times larger than nstpcouple*dt (0.2)


NOTE 3 [file prod1.mdp]:
  The switch/shift interaction settings are just for compatibility; you
  will get better performance from applying potential modifiers to your
  interactions!


Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'CL-'

WARNING 2 [file topol.top, line 16]:
  The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
  estimated oscillational period of 9.7e-02 ps, which is less than 5 times
  the time step of 2.0e-02 ps.
  Maybe you forgot to change the constraints mdp option.


WARNING 3 [file prod1.mdp]:
  For proper integration of the Berendsen thermostat, tau-t (0.5) should be
  at least 5 times larger than nsttcouple*dt (0.2)

Number of degrees of freedom in T-Coupling group Protein is 11517.00
Number of degrees of freedom in T-Coupling group Other is 198744.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame         -1 time 50000.000
Using frame at t = 50000 ps
Starting time for run is 0 ps

NOTE 4 [file prod1.mdp]:
  This run will generate roughly 48891 Mb of data


There were 4 notes

There were 3 warnings

-------------------------------------------------------
Program grompp, VERSION 4.6.3
Source code file: /ivec/build/gromacs-4.6.3/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (3), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Here is the mdp file
; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.020
nsteps             = 125000000
; 125 mio steps x 20fs = 2500ns = 10* microsec
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = Protein Other

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 5000
nstenergy                = 5000
; Output frequency and precision for xtc file =
nstxtcout                = 5000
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 = System
; Selection of energy groups =
energygrps               = Protein Other

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = Berendsen
; Groups to couple separately =
tc-grps                  = Protein Other
; Time constant (ps) and reference temperature (K) =
tau_t                    = 0.5  0.5
ref_t                    = 310 310
; Pressure coupling      =
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 2.00
compressibility          = 5e-5
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = no
gen_temp                 = 310
gen_seed                 = 473529

; OPTIONS FOR BONDS     =
constraints              = none
; Type of constraint algorithm =
constraint_algorithm     = Lincs
; Do not constrain the start configuration =
continuation      = yes
; Highest order in the expansion of the constraint coupling matrix =
lincs_order              = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle          = 30