<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi,</div><div> I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature coupling at 325 K( separate coupling for lipid and water) and pressure coupling at 1 atm for 500 ns).</div><div>But, when I started running the NVE simulation by switching off pressure coupling and temperature coupling, the temperature started going down from 325 to almost 2 K very quickly which looks like very unphysical. However, total energy remains conserved . But the temperature is becoming a concern as it is going down to a 0 K. I am not sure whether I am doing some mistake
in the mdp parameter. Any help will be appreciated.</div><div><br></div><div>Here is the part of mdp option I used for running with gromacs-4.0.7</div><div><br></div><div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>; Start time and timestep in ps</div><div>tinit = 0.0</div><div>dt = 0.020</div><div>nsteps = 25000000</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><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 = DPPC Nonlipid</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>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><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 = 500</div><div>nstvout =
500</div><div>nstfout = 0</div><div>; Output frequency for energies to log file and energy file</div><div>nstlog = 500</div><div>nstenergy = 500</div><div>; Output frequency and precision for xtc file</div><div>nstxtcout = 500</div><div>xtc_precision = 100</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 = DPPC Nonlipid</div><div><br></div><div>; NEIGHBORSEARCHING PARAMETERS</div><div><div>; nblist update
frequency</div><div>nstlist = 10</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 = 1.4</div><div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>; Method for doing electrostatics</div><div>coulombtype = Shift</div><div>rcoulomb_switch = 0.0</div><div>rcoulomb = 1.2</div><div>; Relative dielectric constant for the medium and the reaction
field</div><div>epsilon_r = 15</div><div>epsilon_rf = 1</div><div>; Method for doing Van der Waals</div><div>vdw_type = Shift</div><div>; cut-off lengths</div><div>rvdw_switch = 0.9</div><div>rvdw = 1.2</div><div><div>; Apply long range dispersion corrections for Energy and Pressure</div><div>DispCorr = No</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 = 1e-05</div><div>ewald_geometry = 3d</div><div>epsilon_surface = 0</div><div>optimize_fft = no</div><div><div>; Temperature coupling</div><div>tcoupl = no</div><div>; Groups to couple separately</div><div>tc-grps
=</div><div>; Time constant (ps) and reference temperature (K)</div><div>tau-t =</div><div>ref-t =</div><div>; Pressure coupling</div><div>Pcoupl = no</div><div><br></div><div>; Time constant (ps), compressibility (1/bar) and reference P (bar)</div><div>tau-p = 1</div><div>compressibility =</div><div>ref-p =</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><div>; GENERATE
VELOCITIES FOR STARTUP RUN</div><div>gen_vel = yes</div><div>gen_temp = 325</div><div>gen_seed = 473529</div><div><br></div><div>; OPTIONS FOR BONDS</div><div>constraints = none</div><div>; Type of constraint algorithm</div><div>constraint_algorithm = Lincs</div><div>; Do not constrain the start configuration</div><div>continuation = no</div><div>; Use successive overrelaxation to reduce the number of shake iterations</div><div>Shake-SOR = no</div><div>; Relative tolerance of shake</div><div>shake-tol = 0.0001</div><div>; Highest order in the expansion of the constraint
coupling matrix</div><div>lincs_order = 4</div><div>; Number of iterations in the final step of LINCS. 1 is fine for</div><div>; normal simulations, but use 2 to conserve energy in NVE runs.</div><div>; For energy minimization with constraints it should be 4 to 8.</div><div>lincs-iter = 1</div><div><div>; Lincs will write a warning to the stderr if in one step a bond</div><div>; rotates over more degrees than</div><div>lincs_warnangle = 30</div><div>; Convert harmonic bonds to morse potentials</div><div>morse = no</div></div></div><div><br></div><div>Thanks</div><div>Sanku</div></div></div></div></div></div><div style="position:fixed"></div>
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