Hi everybody, I started changing init-step. Now I seem to have another problem. When I go to switch to another 'block' it tells me that my input and checkpoint states are not identical when I use mdrun the second time. I am not sure how they can be any different as I only have one .cpt file in the directory.
My list of commands is right here - grompp -f 1step.mdp -c 315monolayer.gro -p dppc_monolayer.top -o 315monolayer.tpr mdrun -nt 4 -s 315monolayer.tpr -c 315monolayer.gro -e 315monolayer.edr -o 315monolayer.trr -x 315monolayer.xtc -g 315monolayer.log -cpo 315monolayer.cpt -rdd 2.5 grompp -f 10step.mdp -c 315monolayer.tpr -p dppc_monolayer.top -o 315monolayer.tpr -t 315monolayer.cpt mdrun -nt 4 -s 315monolayer.tpr -c 315monolayer.gro -e 315monolayer.edr -o 315monolayer.trr -x 315monolayer.xtc -g 315monolayer.log -cpi 315monolayer.cpt -cpo 315monolayer.cpt -rdd 2.5 Is there something I am doing wrong with continuing this simulation? This is the saving each step copy of the mdp file: ; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0.0 dt = 0.02 nsteps = 10 init-step = 0 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = DPPC W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1 nstvout = 1 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5 nstenergy = 10 ; Output frequency and precision for xtc file = nstxtcout = 10 xtc_precision = 10 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = DPPC W ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = DPPC W ; Time constant (ps) and reference temperature (K) = tau_t = 1.0 1.0 ref_t = 310 310 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 1.0 1.0 compressibility = 3e-5 0.0 ref_p = 0.0 0.0 nstpcouple = 5 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 315 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 The 10step.mdp file is identical except it runs for 90 steps, init-step is 10 and nstxout is 10. I am guessing that this might have something to do with the frequency of writing .cpt files? Otherwise I have no idea why this could be happening. -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-linear-data-output-storage-possible-tp5008858p5009776.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
