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<div>Hi<div><br></div><div>I am having some pressure coupling issues. I have a fairly large protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I run NVE it conserves energy with appropriate parameter settings. If I run NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello Rahman), the system just continuously expands. My parameters are as follows. Any ideas?</div>
<div><br></div><div>Best,</div><div><br></div><div>Ilya</div><div><br></div><div><div>;</div><div>; File 'mdout.mdp' was generated</div><div>; By user: relly (508)</div><div>; On host: <a href="http://master.simprota.com">master.simprota.com</a></div>
<div>; At date: Fri Mar 6 20:17:33 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>nsteps = 2500000</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>; OUTPUT CONTROL OPTIONS</div><div>; Output frequency for coords (x), velocities (v) and forces (f)</div><div>nstxout = 0</div><div>nstvout = 0</div><div>nstfout = 0</div>
<div> </div><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 = 250</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 = protein</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 = 1.0</div><div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>; Method for doing electrostatics</div><div>coulombtype = PME</div><div>rcoulomb-switch = .9</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 = .9</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><div>; OPTIONS FOR WEAK COUPLING ALGORITHMS</div><div>; Temperature coupling </div><div>Tcoupl = V-rescale</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 = Berendsen</div><div>Pcoupltype = Isotropic</div><div>; Time constant (ps), compressibility (1/bar) and reference P (bar)</div><div>tau_p = 10 </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>
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