<div>I'm using version 4.0.4. Here's my .mdp file:</div>
<div> </div>
<div> </div>
<div>; VARIOUS PREPROCESSING OPTIONS<br>; Preprocessor information: use cpp syntax.<br>; e.g.: -I/home/joe/doe -I/home/mary/hoe<br>include = <br>; e.g.: -DI_Want_Cookies -DMe_Too<br>define = -DPOSRES</div>
<div>; RUN CONTROL PARAMETERS<br>integrator = md<br>; Start time and timestep in ps<br>tinit = 0<br>dt = 0.002<br>nsteps = 10000000<br>; For exact run continuation or redoing part of a run<br>
; Part index is updated automatically on checkpointing (keeps files separate)<br>simulation_part = 1<br>init_step = 0<br>; mode for center of mass motion removal<br>comm-mode = Linear<br>
; number of steps for center of mass motion removal<br>nstcomm = 1<br>; group(s) for center of mass motion removal<br>comm-grps = </div>
<div>; LANGEVIN DYNAMICS OPTIONS<br>; Friction coefficient (amu/ps) and random seed<br>bd-fric = 0<br>ld_seed = 1993</div>
<div>; ENERGY MINIMIZATION OPTIONS<br>; Force tolerance and initial step-size<br>emtol = 0.000001<br>emstep = 0.01<br>; Max number of iterations in relax_shells<br>niter = 100<br>
; Step size (ps^2) for minimization of flexible constraints<br>fcstep = 0<br>; Frequency of steepest descents steps when doing CG<br>nstcgsteep = 1000<br>nbfgscorr = 10</div>
<div>; TEST PARTICLE INSERTION OPTIONS<br>rtpi = 0.05</div>
<div>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f)<br>nstxout = 50000<br>nstvout = 0<br>nstfout = 0<br>; Output frequency for energies to log file and energy file<br>
nstlog = 100<br>nstenergy = 0<br>; Output frequency and precision for xtc file<br>nstxtcout = 10000<br>xtc_precision = 1000<br>; This selects the subset of atoms for the xtc file. You can<br>
; select multiple groups. By default all atoms will be written.<br>xtc-grps = <br>; Selection of energy groups<br>energygrps = </div>
<div>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>nstlist = 10<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz, no, xy<br>pbc = xyz<br>
periodic_molecules = no<br>; nblist cut-off <br>rlist = 1</div>
<div>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = PME<br>rcoulomb_switch = 0<br>rcoulomb = 1.<br>; Relative dielectric constant for the medium and the reaction field<br>
epsilon_r = 1<br>epsilon_rf = 1<br>; Method for doing Van der Waals<br>vdw-type = Cut-off<br>; cut-off lengths <br>rvdw_switch = 0<br>rvdw = 1.0<br>
; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = No<br>; Extension of the potential lookup tables beyond the cut-off<br>table-extension = 1<br>; Seperate tables between energy group pairs<br>
energygrp_table = <br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used<br>fourier_nx = 0<br>fourier_ny = 0<br>
fourier_nz = 0<br>; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = no</div>
<div>; IMPLICIT SOLVENT ALGORITHM<br>implicit_solvent = No</div>
<div>; GENERALIZED BORN ELECTROSTATICS<br>; Algorithm for calculating Born radii<br>gb_algorithm = Still<br>; Frequency of calculating the Born radii inside rlist<br>nstgbradii = 1<br>; Cutoff for Born radii calculation; the contribution from atoms<br>
; between rlist and rgbradii is updated every nstlist steps<br>rgbradii = 2<br>; Dielectric coefficient of the implicit solvent<br>gb_epsilon_solvent = 80<br>; Salt concentration in M for Generalized Born models<br>
gb_saltconc = 0<br>; Scaling factors used in the OBC GB model. Default values are OBC(II)<br>gb_obc_alpha = 1<br>gb_obc_beta = 0.8<br>gb_obc_gamma = 4.85<br>; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA<br>
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.<br>sa_surface_tension = 2.092</div>
<div>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling <br>Tcoupl = v-rescale<br>; Groups to couple separately<br>tc_grps = Protein Other<br>; Time constant (ps) and reference temperature (K)<br>
tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Pressure coupling <br>Pcoupl = Berendsen<br>Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Scaling of reference coordinates, No, All or COM<br>refcoord_scaling = No<br>; Random seed for Andersen thermostat<br>
andersen_seed = 815131</div>
<div>; OPTIONS FOR QMMM calculations<br>QMMM = no<br>; Groups treated Quantum Mechanically<br>QMMM-grps = <br>; QM method <br>QMmethod = <br>; QMMM scheme <br>
QMMMscheme = normal<br>; QM basisset <br>QMbasis = <br>; QM charge <br>QMcharge = <br>; QM multiplicity <br>QMmult = <br>; Surface Hopping <br>
SH = <br>; CAS space options <br>CASorbitals = <br>CASelectrons = <br>SAon = <br>SAoff = <br>SAsteps = <br>; Scale factor for MM charges<br>
MMChargeScaleFactor = 1<br>; Optimization of QM subsystem<br>bOPT = <br>bTS = </div>
<div>; SIMULATED ANNEALING <br>; Type of annealing for each temperature group (no/single/periodic)<br>annealing = no no<br>; Number of time points to use for specifying annealing in each group<br>annealing_npoints = <br>
; List of times at the annealing points for each group<br>annealing_time = <br>; Temp. at each annealing point, for each group.<br>annealing_temp = </div>
<div>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>gen_temp = 300<br>gen_seed = 173529</div>
<div>; OPTIONS FOR BONDS <br>constraints = all-bonds<br>; Type of constraint algorithm<br>constraint_algorithm = Lincs<br>; Do not constrain the start configuration<br>continuation = no<br>
; Use successive overrelaxation to reduce the number of shake iterations<br>Shake-SOR = no<br>; Relative tolerance of shake<br>shake_tol = 1e-04<br>; Highest order in the expansion of the constraint coupling matrix<br>
lincs_order = 4<br>; Number of iterations in the final step of LINCS. 1 is fine for<br>; normal simulations, but use 2 to conserve energy in NVE runs.<br>; For energy minimization with constraints it should be 4 to 8.<br>
lincs-iter = 1<br>; Lincs will write a warning to the stderr if in one step a bond<br>; rotates over more degrees than<br>lincs_warnangle = 30<br>; Convert harmonic bonds to morse potentials<br>morse = no</div>
<div>; ENERGY GROUP EXCLUSIONS<br>; Pairs of energy groups for which all non-bonded interactions are excluded<br>energygrp_excl = </div>
<div>; WALLS <br>; Number of walls, type, atom types, densities and box-z scale factor for Ewald<br>nwall = 0<br>wall_type = 9-3<br>wall_r_linpot = -1<br>wall_atomtype = <br>
wall_density = <br>wall_ewald_zfac = 3</div>
<div>; COM PULLING<br>; Pull type: no, umbrella, constraint or constant_force<br>pull = umbrella<br>; Pull geometry: distance, direction, cylinder or position<br>pull_geometry = distance<br>
; Select components for the pull vector. default: Y Y Y<br>pull_dim = Y Y Y<br>; Cylinder radius for dynamic reaction force groups (nm)<br>pull_r1 = 1<br>; Switch from r1 to r0 in case of dynamic reaction force<br>
pull_r0 = 1.5<br>pull_constr_tol = 1e-06<br>pull_start = yes<br>pull_nstxout = 10<br>pull_nstfout = 1<br>; Number of pull groups<br>pull_ngroups = 1<br>
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)<br>pull_group0 = GRP2<br>pull_weights0 =<br>pull_pbcatom0 = 0<br>pull_group1 = GRP1<br>pull_weights1 =<br>
pull_pbcatom1 = 0<br>pull_vec1 = 0.0 0.0 0.0<br>pull_init1 = 0.0<br>pull_rate1 = 0<br>pull_k1 = 1000<br>pull_kB1 = 0</div>
<div>; NMR refinement stuff <br>; Distance restraints type: No, Simple or Ensemble<br>disre = simple<br>; Force weighting of pairs in one distance restraint: Conservative or Equal<br>disre_weighting = Equal<br>
; Use sqrt of the time averaged times the instantaneous violation<br>disre_mixed = no<br>disre_fc = 1000<br>disre_tau = 1.25<br>; Output frequency for pair distances to energy file<br>
nstdisreout = 100<br>; Orientation restraints: No or Yes<br>orire = no<br>; Orientation restraints force constant and tau for time averaging<br>orire-fc = 0<br>orire-tau = 0<br>
orire-fitgrp = <br>; Output frequency for trace(SD) and S to energy file<br>nstorireout = 100<br>; Dihedral angle restraints: No or Yes<br>dihre = No<br>dihre-fc = 1000</div>
<div>; Free energy control stuff<br>free_energy = no<br>init_lambda = 0<br>delta_lambda = 0<br>sc-alpha = 0<br>sc-power = 0<br>sc-sigma = 0.3<br>
couple-moltype = <br>couple-lambda0 = vdw-q<br>couple-lambda1 = vdw-q<br>couple-intramol = no</div>
<div>; Non-equilibrium MD stuff<br>acc-grps = <br>accelerate = <br>freezegrps = <br>freezedim = <br>cos-acceleration = 0<br>deform = </div>
<div>; Electric fields <br>; Format is number of terms (int) and for all terms an amplitude (real)<br>; and a phase angle (real)<br>E-x = <br>E-xt = <br>E-y = <br>
E-yt = <br>E-z = <br>E-zt = </div>
<div>; User defined thingies<br>user1-grps = <br>user2-grps = <br>userint1 = 0<br>userint2 = 0<br>userint3 = 0<br>userint4 = 0<br>
userreal1 = 0<br>userreal2 = 0<br>userreal3 = 0<br>userreal4 = 0<br><br><br></div>
<div class="gmail_quote">2009/4/20 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">Lee Soin wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello!<br>I'm experiencing a strange thing. I've tried to set nstenergy in .mdp file to various values(0, 1, 1000000) but there seems to be no change in the output frequency in energy file and the file always attains several gigabytes easily. Probably a bug?<br>
</blockquote><br></div>Probably a mis-use, mis-spelling or a mis-observation :-) I'm not aware of any GROMACS version that had such a problem, and you'd have to be able to reproduce it in GROMACS 4.0.4 and at least post your .mdp file before it might be consistent with a bug.<br>
<font color="#888888"><br>Mark</font>
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