<P>Dear USERS,</P>
<P>I met two problems with messages: </P>
<P>1) Fatal error: could not write energies: Invalid argument <BR></P>
<P>2) Warning: pressure scaling more than 1%, mu: 1 1 1.01293<BR>I belived this could be due to tau_p was too small, but it did not help after increase tau_p to 5.0. </P>
<P>My mdp file is as follows:</P><FONT size=2>
<P>integrator = md</P>
<P>; start time and timestep in ps</P>
<P>tinit = 0.0</P>
<P>dt = 0.002</P>
<P>nsteps = 2000</P>
<P>; mode for center of mass motion removal</P>
<P>comm-mode = Linear</P>
<P>; number of steps for center of mass motion removal</P>
<P>nstcomm = 1</P>
<P>; group(s) for center of mass motion removal</P>
<P>comm-grps = </P>
<P>;</P>
<P>; LANGEVIN DYNAMICS OPTIONS</P>
<P>; Temperature, friction coefficient (amu/ps) and random seed</P>
<P>bd-temp = 300</P>
<P>bd-fric = 0</P>
<P>ld_seed = 1993</P>
<P>;</P>
<P>; ENERGY MINIMIZATION OPTIONS</P>
<P>; Force tolerance and initial step-size</P>
<P>emtol = 1; 0.001</P>
<P>emstep = 0.1</P>
<P>; Max number of iterations in relax_shells</P>
<P>niter = 100</P>
<P>; Step size (1/ps^2) for minimization of flexible constraints</P>
<P>fcstep = 0</P>
<P>; Frequency of steepest descents steps when doing CG</P>
<P>nstcgsteep = 1000</P>
<P>;</P>
<P>; OUTPUT CONTROL OPTIONS</P>
<P>; Output frequency for coords (x), velocities (v) and forces (f)</P>
<P>nstxout = 20</P>
<P>nstvout = 20</P>
<P>nstfout = 0</P>
<P>; Checkpointing helps you continue after crashes</P>
<P>;nstcheckpoint = 1000 </P>
<P>; Output frequency for energies to log file and energy file</P>
<P>nstlog = 0</P>
<P>nstenergy = 1</P>
<P>; Output frequency and precision for xtc file</P>
<P>nstxtcout = 0</P>
<P>xtc_precision = 1000</P>
<P>; This selects the subset of atoms for the xtc file. You can</P>
<P>; select multiple groups. By default all atoms will be written.</P>
<P>xtc-grps = </P>
<P>; Selection of energy groups</P>
<P>energygrps = system</P>
<P>;</P>
<P>; NEIGHBORSEARCHING PARAMETERS</P>
<P>; nblist update frequency</P>
<P>nstlist = 1</P>
<P>; ns algorithm (simple or grid)</P>
<P>ns_type = simple</P>
<P>; Periodic boundary conditions: xyz or no</P>
<P>pbc = xyz</P>
<P>; nblist cut-off </P>
<P>rlist = 1.0</P>
<P>;domain-decomposition = no ;</P>
<P>;</P>
<P>; OPTIONS FOR ELECTROSTATICS AND VDW</P>
<P>; Method for doing electrostatics</P>
<P>coulombtype = Cut-off</P>
<P>rcoulomb_switch = 0 ;</P>
<P>rcoulomb = 1.0</P>
<P>; Dielectric constant (DC) for cut-off or DC of reaction field</P>
<P>epsilon_r = 1</P>
<P>; Method for doing Van der Waals</P>
<P>vdw-type = Cut-off</P>
<P>; cut-off lengths </P>
<P>rvdw_switch = 0 ;</P>
<P>rvdw = 1.0</P>
<P>; Apply long range dispersion corrections for Energy and Pressure</P>
<P>DispCorr = No</P>
<P>; Spacing for the PME/PPPM FFT grid</P>
<P>fourierspacing = 0.12</P>
<P>; FFT grid size, when a value is 0 fourierspacing will be used</P>
<P>fourier_nx = 10</P>
<P>fourier_ny = 10</P>
<P>fourier_nz = 10</P>
<P>; EWALD/PME/PPPM parameters</P>
<P>pme_order = 4</P>
<P>ewald_rtol = 1e-05</P>
<P>ewald_geometry = 3d</P>
<P>surface_epsilon = 0 ; </P>
<P>optimize_fft = no</P>
<P>;</P>
<P>; GENERALIZED BORN ELECTROSTATICS</P>
<P>; Algorithm for calculating Born radii</P>
<P>;gb_algorithm = Still ;</P>
<P>; Frequency of calculating the Born radii inside rlist</P>
<P>;nstgbradii = 1 ;</P>
<P>; Cutoff for Born radii calculation; the contribution from atoms</P>
<P>; between rlist and rgbradii is updated every nstlist steps</P>
<P>;rgbradii = 2 ;</P>
<P>; Salt concentration in M for Generalized Born models</P>
<P>;gb_saltconc = 0 ;</P>
<P>;</P>
<P>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)</P>
<P>;implicit_solvent = No ;</P>
<P>; OPTIONS FOR WEAK COUPLING ALGORITHMS</P>
<P>; Temperature coupling </P>
<P>tcoupl = no</P>
<P>; Groups to couple separately</P>
<P>;Pressure coupling </P>
<P>Pcoupl = berendsen ;</P>
<P>Pcoupltype = surface-tension</P>
<P>tau_p = 5.0 5.0 ;</P>
<P>compressibility = 4.5e-18 4.5e-1 ; </P>
<P>ref_p = 0.0 2.0 ; </P>
<P>; </P>
<P>; Random seed for Andersen thermostat</P>
<P>;andersen_seed = 815131 ;</P>
<P>;</P>
<P>; Type of annealing for each temperature group (no/single/periodic)</P>
<P>annealing = no</P>
<P>; Number of time points to use for specifying annealing in each group</P>
<P>annealing_npoints = </P>
<P>; List of times at the annealing points for each group</P>
<P>annealing_time = </P>
<P>; Temp. at each annealing point, for each group.</P>
<P>annealing_temp = </P>
<P>; GENERATE VELOCITIES FOR STARTUP RUN</P>
<P>gen_vel = no</P>
<P>gen_temp = 120</P>
<P>gen_seed = 173529</P>
<P>; OPTIONS FOR BONDS </P>
<P>constraints = none</P>
<P>; Type of constraint algorithm</P>
<P>constraint_algorithm = Lincs</P>
<P>; Do not constrain the start configuration</P>
<P>unconstrained_start = no</P>
<P>; Use successive overrelaxation to reduce the number of shake iterations</P>
<P>Shake-SOR = no</P>
<P>; Relative tolerance of shake</P>
<P>shake_tol = 0.0001</P>
<P>; Highest order in the expansion of the constraint coupling matrix</P>
<P>lincs_order = 4</P>
<P>; Number of iterations in the final step of LINCS. 1 is fine for</P>
<P>; normal simulations, but use 2 to conserve energy in NVE runs.</P>
<P>; For energy minimization with constraints it should be 4 to 8.</P>
<P>lincs-iter = 1 ;</P>
<P>; Lincs will write a warning to the stderr if in one step a bond</P>
<P>; rotates over more degrees than</P>
<P>lincs_warnangle = 30</P>
<P>; Convert harmonic bonds to morse potentials</P>
<P>morse = no</P>
<P>; ENERGY GROUP EXCLUSIONS</P>
<P>; Pairs of energy groups for which all non-bonded interactions are excluded</P>
<P>energygrp_excl = </P>
<P>; NMR refinement stuff </P>
<P>; Distance restraints type: No, Simple or Ensemble</P>
<P>disre = No</P>
<P>; Force weighting of pairs in one distance restraint: Conservative or Equal</P>
<P>disre_weighting = Equal</P>
<P>; Use sqrt of the time averaged times the instantaneous violation</P>
<P>disre_mixed = no</P>
<P>disre_fc = 1000</P>
<P>disre_tau = 1.25</P>
<P>; Output frequency for pair distances to energy file</P>
<P>nstdisreout = 100</P>
<P>; Orientation restraints: No or Yes</P>
<P>orire = no</P>
<P>; Orientation restraints force constant and tau for time averaging</P>
<P>orire-fc = 0</P>
<P>orire-tau = 0</P>
<P>orire-fitgrp = </P>
<P>; Output frequency for trace(SD) to energy file</P>
<P>nstorireout = 100</P>
<P>; Dihedral angle restraints: No, Simple or Ensemble</P>
<P>;dihre = No ;</P>
<P>;dihre-fc = 1000 ;</P>
<P>;dihre-tau = 0</P>
<P>; Output frequency for dihedral values to energy file</P>
<P>;nstdihreout = 100 ; </P>
<P>; Free energy control stuff</P>
<P>free_energy = no</P>
<P>init_lambda = 0</P>
<P>delta_lambda = 0</P>
<P>sc-alpha = 0</P>
<P>sc-sigma = 0.3</P>
<P>; Non-equilibrium MD stuff</P>
<P>acc-grps = ; </P>
<P>accelerate = ; </P>
<P>freezegrps = ;</P>
<P>freezedim = ;</P>
<P>cos-acceleration = 0</P>
<P> </P>
<P>Your advice is greatly appreciated. Thanks </P>
<P>Albert</P></FONT><p><hr SIZE=1>
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