<div dir="ltr">Hi, gmx-users:<div> I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. </div><div> I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours.</div>
<div> Here is the .mdp file: </div><div>define =</div><div>; RUN CONTROL PARAMETERS =</div><div>integrator = sd</div><div>; start time and timestep in ps =</div><div>tinit = 0</div>
<div>dt = 0.001</div><div>nsteps = 200000</div><div>; number of steps for center of mass motion removal =</div><div>nstcomm = 100</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>; Output frequency for energies to log file and energy file =</div>
<div>nstlog = 100</div><div>nstenergy = 100</div><div>; Output frequency and precision for xtc file =</div><div>nstxtcout = 100</div><div>xtc-precision = 1000</div>
<div>; NEIGHBORSEARCHING PARAMETERS =</div><div>; nblist update frequency =</div><div>nstlist = 50</div><div>; ns algorithm (simple or grid) =</div><div>ns_type = grid</div><div><br></div>
<div>;OPTIONS FOR PRESSURE COUPLING</div><div>Pcoupl = berendsen</div><div>tau_p = 1</div><div>compressibility = 4.5e-05</div><div>ref_p = 0.1</div><div>;OPTIONS FOR TEMPERATURE COUPLING</div>
<div>tc_grps = system</div><div>tau_t = 0.1</div><div>ref_t = 300</div><div>; OPTIONS FOR BONDS =</div><div>constraints = hbonds</div><div>; Type of constraint algorithm =</div>
<div>constraint-algorithm = Lincs</div><div>; Do not constrain the start configuration =</div><div>unconstrained-start = 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 = 12</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>; Periodic boundary conditions: xyz, no, xy</div><div>pbc = xyz</div><div>periodic_molecules = no</div><div>; nblist cut-off </div><div>rlist = 1</div>
<div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>; Method for doing electrostatics</div><div>coulombtype = Ewald</div><div>rcoulomb = 1</div><div>; Method for doing Van der Waals</div>
<div>vdw-type = Cut-off</div><div>; cut-off lengths </div><div>rvdw = 1</div><div><br></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 = 6</div><div>ewald_rtol = 1e-4</div><div>ewald_geometry = 3d</div><div>epsilon_surface = 0</div><div>optimize_fft = no</div><div><br></div><div>
Can anyone help me? Thank you in advance.</div>
<div>Thanks,<br>Shuangxing Dai<br>
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