Hi there,<br><br>I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = <blank> and comm-grps = carb and what is below.<br>
<br>carb is the name I use in my top file and index file. For the index I specify the groups in make_ndx and then text edit the index file and change the name to carb. I've run this simulation on a different carb before but with integrator set to md and it worked fine. <br>
<br>Any help would be very welcome<br><br>Oliver<br><br><br><br><br> RUN CONTROL PARAMETERS<br>integrator = sd<br>; Start time and timestep in ps<br>tinit = 0<br>dt = 0.002<br>
nsteps = 100000000<br>; For exact run continuation or redoing part of a run<br>init_step = 0<br>; mode for center of mass motion removal<br>comm-mode = Linear<br>; number of steps for center of mass motion removal<br>
nstcomm = 1<br>; group(s) for center of mass motion removal<br>comm-grps = carb SOL Na<br><br>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f)<br>
nstxout = 5000<br>nstvout = 10000<br>nstfout = 10000<br>; Checkpointing helps you continue after crashes<br>nstcheckpoint = 5000<br>; Output frequency for energies to log file and energy file<br>
nstlog = 5000<br>nstenergy = 5000<br>; Output frequency and precision for xtc file<br>nstxtcout = 0<br>xtc-precision = 0<br>; This selects the subset of atoms for the xtc file. You can<br>
; select multiple groups. By default all atoms will be written.<br>xtc-grps = <br>; Selection of energy groups<br>energygrps = <br><br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>
nstlist = 5<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz (default), no (vacuum)<br>; or full (infinite systems only)<br>pbc = xyz<br>
; nblist cut-off <br>rlist = 0.9<br>domain-decomposition = no<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = PME<br>rcoulomb-switch = 0<br>
rcoulomb = 0.9<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = cut-off<br>; cut-off lengths <br>
rvdw-switch = 0<br>rvdw = 0.9<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Extension of the potential lookup tables beyond the cut-off<br>
table-extension = 1<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used<br>fourier_nx = 0<br>fourier_ny = 0<br>
fourier_nz = 0<br>; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = no<br>
<br><br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling <br>Tcoupl = berendsen<br>; Groups to couple separately<br>tc-grps = carb SOL Na<br>; Time constant (ps) and reference temperature (K)<br>
tau_t = 0.1 0.1 0.1<br>ref_t = 300 300 300<br>; Pressure coupling <br>Pcoupl = berendsen<br>Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Random seed for Andersen thermostat<br>andersen_seed = 815131<br><br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>
gen_vel = no<br>gen_temp = 300<br>gen_seed = 1993<br><br>; OPTIONS FOR BONDS <br>constraints = none<br>; Type of constraint algorithm<br>constraint-algorithm = Lincs<br>
; Do not constrain the start configuration<br>unconstrained-start = no<br>; Use successive overrelaxation to reduce the number of shake iterations<br>Shake-SOR = no<br>; Relative tolerance of shake<br>
shake-tol = 1e-04<br>; Highest order in the expansion of the constraint coupling matrix<br>lincs-order = 4<br>; Number of iterations in the final step of LINCS. 1 is fine for<br>; normal simulations, but use 2 to conserve energy in NVE runs.<br>
; For energy minimization with constraints it should be 4 to 8.<br>lincs-iter = 1<br>; Lincs will write a warning to the stderr if in one step a bond<br>; rotates over more degrees than<br>lincs-warnangle = 30<br>
; Convert harmonic bonds to morse potentials<br>morse = no<br><br><br>