> Can you post the relevant .mdp file(s)? Are you preserving velocity > information from the previous trajectory, or generating new velocities? Are > any of the species in your system constrained? > > -Justin >
I usually use the final output file generated by GROMACS which contain the velocity. But, I dont preserve the velocity every timestep. CNT, CMT are constrained. I would want to make them move only in X direction, but I cannot make the simulation work even when they are constrained. title = Yo cpp = /usr/bin/cpp include = -I/home/rajesh/gromacs_forcefield/FMN ;include = -I/cygdrive/c/cygwin/gromacs_forcefield/FMN_force_field define = ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; start time dt = 0.002 ; time step nsteps = 5000 ; number of steps init_step = 0 ; For exact run continuation or redoing part of a run comm-mode = None ; mode for center of mass motion removal nstcomm = 1 ; number of steps for center of mass motion removal comm-grps = ; group(s) for center of mass motion removal ; ENERGY MINIMIZATION OPTIONS emtol = 100 ; Force tolerance emstep = 0.1 ; initial step-size niter = 20000 ; Max number of iterations in relax_shells fcstep = 0 ; Step size (1/ps^2) for minimization of flexible constraints nstcgsteep = 1000 ; Frequency of steepest descents steps when doing CG nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS nstxout = 100 ; coordinates nstvout = 0 ; velocities nstfout = 0 ; forces nstcheckpoint = 10000 ; Checkpointing helps you continue after crashes nstlog = 100 ; Output frequency for energies to log file nstenergy = 1000 ; Output frequency for energies to energy file nstxtcout = 00 ; Output frequency for xtc file xtc-precision = 10000 ; Output precision for xtc file ; This selects the subset of atoms for the xtc file. You can xtc-grps = FMN SOD ; select multiple groups. By default all atoms will be written. energygrps = FMN CNT SOD CMT SOL ; Selection of energy groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; nblist update frequency ns_type = grid ; ns algorithm (simple or grid) pbc = xyz ; Periodic boundary conditions: xyz (default), no (vacuum);; or full (infinite systems only) rlist = 1.4 ; nblist cut-off domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME ; Method for doing electrostatics rcoulomb-switch = rcoulomb = 1.4 epsilon-r = 1 ; Dielectric constant (DC) for cut-off or DC of reaction field vdw-type = switch ; Method for doing Van der Waals rvdw-switch = 1.2 ; cut-off lengths rvdw = 1.4 DispCorr = EnerPres ; Apply long range dispersion corrections for Energy and Pressure table-extension = 1 ; Extension of the potential lookup tables beyond the cut-off fourierspacing = 0.12 ; Spacing for the PME/PPPM FFT grid fourier_nx = 0 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = nose-hoover ; Temperature coupling tc-grps = System ; Groups to couple separately tau_t = 0.1 ; Time constant (ps) ref_t = 300 ; Reference temperature (K) Pcoupl = no ; Pressure coupling Pcoupltype = semiisotropic tau_p = 0.5 0.0 ; Time constant (ps), compressibility (1/bar) and reference P (bar) compressibility = 4.5e-5 0.0 ref_p = 1.0 0.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = none constraint-algorithm = lincs ; Type of constraint algorithm unconstrained-start = no ; Do not constrain the start configuration Shake-SOR = no ; Use successive overrelaxation to reduce the number of shake iterations shake-tol = 1e-04 ; Relative tolerance of shake lincs-order = 4 ; Highest order in the expansion of the constraint coupling matrix ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 lincs-warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates over more degrees than morse = no ; Convert harmonic bonds to morse potentials ; ENERGY GROUP EXCLUSIONS energygrp_excl = CNT CNT CMT CMT ; Pairs of energy groups for which all non-bonded interactions are excluded ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 nstdihreout = 100 ; Output frequency for dihedral values to energy file ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = CNT CMT freezedim = Y Y Y Y Y Y cos-acceleration = 0 > > Thanks >> Rajesh >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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