[gmx-users] Martini in Gromacs
Justin Lemkul
jalemkul at vt.edu
Tue Jun 10 16:28:55 CEST 2014
On 6/10/14, 8:44 AM, Neha Gandhi 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
> -------------------------------------------------------
>
Simply put, your settings aren't robust. grompp is telling you the way to fix
the settings related to the thermostat and barostat. With respect to the time
step, you're right on the verge of stability. The assigned parameters indicate
that the bond oscillates a bit too quickly for the chosen time step. Other
notes indicate that there are likely better algorithms that can be chosen.
-Justin
> 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
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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