[gmx-users] MD for DNA structure
Justin Lemkul
jalemkul at vt.edu
Thu Oct 30 13:03:45 CET 2014
On 10/30/14 5:22 AM, Urszula Uciechowska wrote:
> Dear Gromacs users,
>
> I am trying to run MD for my DNA structure, however after typing
>
> grompp -f nvt.mdp -c em.gor -p top -o *.tpr
>
> I am getting an error message:
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
>
> NOTE 1 [file nvt.mdp]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat.
>
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'DNA'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
> Setting gen_seed to 17417
> Velocities were taken from a Maxwell distribution at 310 K
> Analysing residue names:
> There are: 46 DNA residues
> There are: 39061 Water residues
> There are: 190 Ion residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.3
> Source code file: readir.c, line: 1316
>
> Fatal error:
> Group Non-Protein not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the
> '-n' option of grompp.
> In that case use the '-n' option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> My nvt.mdp file contains:
>
> 7.3.2 Preprocessing
> define = -DPOSRES ; defines to pass to the preprocessor
>
> ; 7.3.3 Run Control
> integrator = md ; md integrator
> tinit = 0 ; [ps] starting time for run
> dt = 0.002 ; [ps] time step for
> integration
> nsteps = 100000 ; maximum number of steps
> to integrate, 0.002 * 25,000 = 50 ps
> comm_mode = Linear ; remove center of mass
> translation
> nstcomm = 1 ; [steps] frequency of
> mass motion removal
> comm_grps = Non-Protein ; group(s) for center of
> mass motion removal
>
> ; 7.3.8 Output Control
> nstxout = 25000 ; [steps] freq to write
> coordinates to trajectory
> nstvout = 25000 ; [steps] freq to write velocities
> to trajectory
> nstfout = 25000 ; [steps] freq to write forces to
> trajectory
> nstlog = 100 ; [steps] freq to write energies
> to log file
> nstenergy = 100 ; [steps] freq to write energies
> to energy file
> nstxtcout = 100 ; [steps] freq to write
> coordinates to xtc trajectory
> xtc_precision = 1000 ; [real] precision to write xtc
> trajectory
> xtc_grps = System ; group(s) to write to xtc trajectory
> energygrps = System ; group(s) to write to energy file
>
> ; 7.3.9 Neighbor Searching
> nstlist = 1 ; [steps] freq to update neighbor
> list
> ns_type = grid ; method of updating neighbor list
> pbc = xyz ; periodic boundary conditions in
> all directions
> rlist = 0.8 ; [nm] cut-off distance for the
> short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype = PME ; Particle-Mesh Ewald electrostatics
> rcoulomb = 0.8 ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype = cut-off ; twin-range cut-off with rlist
> where rvdw >= rlist
> rvdw = 0.8 ; [nm] distance for LJ cut-off
> DispCorr = EnerPres ; apply long range dispersion
> corrections
>
> ; 7.3.13 Ewald
> fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
> when using PME
> pme_order = 4 ; interpolation order for PME, 4 =
> cubic
> ewald_rtol = 1e-5 ; relative strength of
> Ewald-shifted potential at rcoulomb
> ; 7.3.14 Temperature Coupling
> tcoupl = berendsen ; temperature
> coupling with Berendsen-thermostat
> tc_grps = Non-Protein ; groups to couple
> seperately to temperature bath
> tau_t = 0.1 ; [ps] time
> constant for coupling
> ref_t = 310 ; [K] reference
> temperature for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel = yes ; generate velocities according to
> Maxwell distribution of temperature
> gen_temp = 310 ; [K] temperature for Maxwell
> distribution
> gen_seed = -1 ; [integer] used to initialize
> random generator for random velocities
>
> ; 7.3.18 Bonds
> constraints = all-bonds ; convert all bonds to constraints
> constraint_algorithm = LINCS ; LINear Constraint Solver
> continuation = no ; no = apply constraints to the
> start configuration
> lincs_order = 4 ; highest order in the expansion
> of the contraint coupling matrix
> lincs_iter = 1 ; number of iterations to correct
> for rotational lengthening
> lincs_warnangle = 30 ; [degrees] maximum angle that a
> bond can rotate before LINCS will complain
>
> What can be wrong? I did not have problems with energy minimization.
>
If you don't have Protein, you can't use Non-Protein. Your system is DNA and
solvent, so your groups should reflect that. Run make_ndx on your coordinate
file to see the default groups that are accessible to you.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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