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
Thanks in advance!
Regards,
Kester
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