Hi,<div><br></div><div>I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below.</div><div>
<br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><br></div><div><br></div><div><div>;</div><div>; File 'mdout.mdp' was generated</div><div>; By user: ichorny (502)</div><div>; On host: <a href="http://master.simprota.com">master.simprota.com</a></div>
<div>; At date: Tue Mar 31 18:01:39 2009</div><div>;</div><div><br></div><div>; VARIOUS PREPROCESSING OPTIONS</div><div>; Preprocessor information: use cpp syntax.</div><div>; e.g.: -I/home/joe/doe -I/home/mary/hoe</div>
<div>include =</div><div>; e.g.: -DI_Want_Cookies -DMe_Too</div><div>define =</div><div><br></div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>; Start time and timestep in ps</div>
<div>tinit = 0</div><div>dt = 0.004</div><div>nsteps = 250000</div><div>; For exact run continuation or redoing part of a run</div><div>; Part index is updated automatically on checkpointing (keeps files separate)</div>
<div>simulation_part = 1</div><div>init_step = 0</div><div>; mode for center of mass motion removal</div><div>comm_mode = linear</div><div>; number of steps for center of mass motion removal</div>
<div>nstcomm = 1</div><div>; group(s) for center of mass motion removal</div><div>comm_grps = system</div><div><br></div><div>; LANGEVIN DYNAMICS OPTIONS</div><div>; Friction coefficient (amu/ps) and random seed</div>
<div>bd-fric = 0</div><div>ld-seed = 1993</div><div><br></div><div>; ENERGY MINIMIZATION OPTIONS</div><div>; Force tolerance and initial step-size</div><div>emtol = 10</div>
<div>emstep = 0.01</div><div>; Max number of iterations in relax_shells</div><div><div>niter = 20</div><div>; Step size (ps^2) for minimization of flexible constraints</div><div>fcstep = 0</div>
<div>; Frequency of steepest descents steps when doing CG</div><div>nstcgsteep = 1000</div><div>nbfgscorr = 10</div><div><br></div><div>; TEST PARTICLE INSERTION OPTIONS</div><div>rtpi = 0.05</div>
<div><br></div><div>; OUTPUT CONTROL OPTIONS</div><div>; Output frequency for coords (x), velocities (v) and forces (f)</div><div>nstxout = 100000</div><div>nstvout = 0</div><div>nstfout = 0</div>
<div>; Output frequency for energies to log file and energy file</div><div>nstlog = 10</div><div>nstenergy = 10</div><div>; Output frequency and precision for xtc file</div><div>nstxtcout = 5000</div>
<div>xtc-precision = 1000</div><div>; This selects the subset of atoms for the xtc file. You can</div><div>; select multiple groups. By default all atoms will be written.</div><div>xtc-grps =</div>
<div>; Selection of energy groups</div><div>energygrps =</div><div><br></div><div>; NEIGHBORSEARCHING PARAMETERS</div><div>; nblist update frequency</div><div>nstlist = 5</div><div>; ns algorithm (simple or grid)</div>
<div>ns_type = grid</div><div>; Periodic boundary conditions: xyz, no, xy</div><div>pbc = xyz</div><div>periodic_molecules = no</div><div>; nblist cut-off</div><div>rlist = 1.1</div>
<div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostatics</div><div>coulombtype = pme-switch</div><div>rcoulomb-switch = .85</div><div>rcoulomb = 1.0</div>
<div>; Relative dielectric constant for the medium and the reaction field</div><div>epsilon-r = 80</div><div>epsilon_rf = 1</div><div>; Method for doing Van der Waals</div><div>vdw-type = Switch</div>
<div>; cut-off lengths</div><div>rvdw-switch = .85</div><div>rvdw = 1.0</div><div>; Apply long range dispersion corrections for Energy and Pressure</div><div>DispCorr = EnerPres</div>
<div>; Extension of the potential lookup tables beyond the cut-off</div><div>table-extension = 1</div><div>; Seperate tables between energy group pairs</div><div>energygrp_table = </div><div>; Spacing for the PME/PPPM FFT grid</div>
<div>fourierspacing = 0.12</div><div>; FFT grid size, when a value is 0 fourierspacing will be used</div><div>fourier_nx = 0 </div><div>fourier_ny = 0 </div><div>fourier_nz = 0</div>
<div>; EWALD/PME/PPPM parameters</div><div>pme_order = 4</div><div>ewald_rtol = 1.e-05</div><div>ewald_geometry = 3d</div><div>epsilon_surface = 0</div><div>optimize_fft = no</div>
<div><br></div><div>; IMPLICIT SOLVENT ALGORITHM</div><div>implicit_solvent = No</div><div><br></div><div>; GENERALIZED BORN ELECTROSTATICS</div><div>; Algorithm for calculating Born radii</div><div>gb_algorithm = Still</div>
<div>; Frequency of calculating the Born radii inside rlist</div><div>nstgbradii = 1 </div><div><br></div><div><div>; Cutoff for Born radii calculation; the contribution from atoms</div><div>; between rlist and rgbradii is updated every nstlist steps</div>
<div>rgbradii = 2</div><div>; Dielectric coefficient of the implicit solvent</div><div>gb_epsilon_solvent = 80</div><div>; Salt concentration in M for Generalized Born models</div><div>gb_saltconc = 0</div>
<div>; Scaling factors used in the OBC GB model. Default values are OBC(II)</div><div>gb_obc_alpha = 1</div><div>gb_obc_beta = 0.8</div><div>gb_obc_gamma = 4.85</div><div>; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA</div>
<div>; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.</div><div>sa_surface_tension = 2.092</div><div><br></div><div>; OPTIONS FOR WEAK COUPLING ALGORITHMS</div><div>; Temperature coupling</div><div>
Tcoupl = no</div><div>; Groups to couple separately</div><div>tc-grps = System</div><div>; Time constant (ps) and reference temperature (K)</div><div>tau_t = 0.1</div>
<div>ref_t = 298.0</div><div>; Pressure coupling</div><div>Pcoupl = No</div><div>Pcoupltype = Isotropic</div><div>; Time constant (ps), compressibility (1/bar) and reference P (bar)</div>
<div>tau_p = 1.67</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.01325</div><div>; Scaling of reference coordinates, No, All or COM</div><div>refcoord_scaling = No</div>
<div>; Random seed for Andersen thermostat</div><div>andersen_seed = 815131</div><div><div>; GENERATE VELOCITIES FOR STARTUP RUN</div><div>gen_vel = yes</div><div>gen_temp = 298.0</div>
<div>gen-seed = 173529</div><div><br></div></div></div><div> </div></div></div>