[gmx-users] charge group moved too far between two domain decomposition step
Mark Abraham
mark.j.abraham at gmail.com
Wed Oct 22 11:13:23 CEST 2014
On Wed, Oct 22, 2014 at 6:37 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:
> Hi Mark,
>
>
> Thanks for the input, I thought a time step of 2 fs is small enough?
>
Not always for unconstrained bonds. The largest stable time step is
determined by the size of the period of the fastest oscillation, which is
vibrations of bonds to hydrogen. 2fs stretches the friendship there, and
you would certainly want to equilibrate thoroughly at a smaller time step
if you are doing messy things like freezing nanotubes and using pressure
coupling (which would not be my go-to method without a clear demonstration
that it produces valid results). More generally, equilibration of a
not-quite-right structure works better with a smaller timestep, because
that copes better with the artificially large forces you get...
> Should I change my constraint to constraints = h-bonds instead?
>
That would be normal.
> Or,
>
>
> Should I use:
>
> dt = 0.001 ; 1 fs
>
> constraints = none
>
> constraint-algorithm = shake
>
Plausible, but you want to run the final simulation with constraints for
the higher ns/day you obtain...
Mark
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 Wong wrote:
>
> > 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
> >
> >
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