Hi Mark,
Thanks for the input, I thought a time step of 2 fs is small enough?
Should I change my constraint to constraints = h-bonds instead?
Or,
Should I use:
dt = 0.001 ; 1 fs
constraints = none
constraint-algorithm = shake
Cheers,
Kester
You should start by using a time step more appropriate to your use of constraints = none, or vice versa. Mark On Wed, Oct 22, 2014 at 4:26 AM, Kester Wongwrote: > Dear all, > > > I am intrigued by the error that I have received this morning, as follows: > > > > The charge group starting at atom 37920 moved more than the distance > allowed by the domain decomposition (1.400000) in direction Y > > distance out of cell 7.144197 > > Old coordinates: 54.499 39.697 14.058 > > New coordinates: 54.499 39.697 14.058 > > Old cell boundaries in direction Y: 19.468 32.846 > > New cell boundaries in direction Y: 18.667 32.553 > > > If the charge group moved, if any, then shouldn't the new coordinates be > showing different values? > > It was a new NPT calculation that I continued from a 20ns NVT run, so it > should be equilibrated well enough, for a simple water on graphene system. > > > Using GROMACS 5.0, I was unable to start the NPT with Berendsen > thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my > tau-T was 0.5, following the general rule of thumb, that tau-P should be > larger than tau-T to allow thermal degrees of freedom to equilibrate faster > than the box size). > > > Should I reduce tau-P? > > > > > Below is my NPT.mdp parameters: > > ; RUN CONTROL PARAMETERS > > integrator = md > > tinit = 20000.000 > > dt = 0.002 ; 2 fs > > nsteps = 5000000 ; 10,000 ps > > comm-mode = Linear > > nstcomm = 10 > > > emtol = 0.001 > > niter = 30 > > > ; OUTPUT CONTROL OPTIONS > > nstxout = 5000 ; save coordinates every 8 ps > > nstvout = 5000 ; save velocities every 8 ps > > nstfout = 0 > > nstlog = 5000 ; update log file every 8 ps > > nstenergy = 5000 ; save energies every 8 ps > > ;nstxtcout is replaced with nstxout-compressed > > nstxout-compressed = 5000 ; no. of steps between writing > coordinates using lossy compression > > ;xtc-precision is replaced with compressed-x-precision > > compressed-x-precision = 3000 ; precision with which to write to the > compressed trajectory file > > > ; Periodic boundary conditions: xyz (default), no (vacuum) > > cutoff-scheme = Verlet ; default for GROMACS-5.0 > > nstlist = 1 ; A smaller nstlist may reduce LINCS > warnings > > ns-type = grid ; > > pbc = xyz > > ;periodic_molecules = yes ; cannot be used with SHAKE > > ; nblist cut-off > > rlist = 1.40 ; short-range neighbourlist cutoff > > nstcalclr = 1 > > > coulombtype = PME > > coulomb-modifier = Potential-shift-Verlet > > r_coulomb = 1.40 ; short-range electrostatic cutoff > > rcoulomb-switch = 0 ; used when potential-switch > (coulomb-modifier) is specified > > epsilon-r = 1 ; default value=1 > > pme_order = 4 > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ewald_rtol = 1e-05 > > ewald_geometry = 3d > > epsilon_surface = 0 ; Use 0 when simulation is done with PME > > > > ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0 > > vdwtype = Cut-off > > vdw_modifier = Potential-switch > > ; cut-off lengths > > rvdw-switch = 1.00 > rvdw = 1.40 ; short-range van der Waals cutoff > > constraints = none > constraint-algorithm = SHAKE > continuation = yes ; starting from NVT run > Shake-SOR = no > shake-tol = 0.0001 > ;lincs-order = 4 ; accuracy of LINCS > ;lincs-iter = 24 ; also related to accuracy > ; Lincs will write a warning to the stderr if in one step a bond > ; rotates over more degrees than > ;lincs-warnangle = 30 > > Tcoupl = v-rescale > nh-chain-length = 1 ; the leapfrog md integrator only supports > 1 > ; Groups to couple separately > tc-grps = GRA SOL > ; Time constant (ps) and reference temperature (K) > tau-t = 0.5 0.5 > ref-t = 300 300 > nsttcouple = 20 ; added by k-wong ; not specified in > Yanbin's MDP > > Pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau-p = 5.0 ; time constant in ps > compressibility = 4.5e-5 ; isothermal compressibility of water, > bar^-1 > ref-p = 1.0 ; reference pressure, in bar > > > ; Non-equilibrium MD stuff > freezegrps = GRA > freezedim = Y Y Y > > gen_vel = no > ;gen_temp = 300 > ;gen_seed = 173529 > > > Thanks in advance! > > > > Regards, > > Kester > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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