[gmx-users] Martini in Gromacs

Dr. Vitaly Chaban vvchaban at gmail.com
Tue Jun 10 16:12:49 CEST 2014


where do you see errors?


Dr. Vitaly V. Chaban


On Tue, Jun 10, 2014 at 2:44 PM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> 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
> --
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