The mdp file is attached.
Best,
Gyorgy
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
gyorgy.han...@fc.up.pt wrote:
Dear all,
I am setting up a simulation of ionic liquids with the PF6 anion.
According to the potential, the anion should be kept rigid, wich
obviously means that bond lengths and angles have to be
constrained. LINCS doesn't work with angle constraints (i.e.
constraing a triangle), so we decided to use SHAKE. However, SHAKE
seems to work a bit strangely: I know SHAKE mustn't be used with
domain decomposition, but even if I set the corresponding variable
to NO in the mdp file, the simulation crashes on 8 procs and gives
the following error message:
Fatal error:
1 particles communicated to PME node 7 are more than a cell length
out of the domain decomposition cell of their charge group.
If I try to run mdrun with -pd (to 'really' switch off domain
decomposition), the simulation doesn't chrash but gives nonsense
(the energy seems to increase constantly).
I am not an expert user so maybe I do something wrong but, anyway,
does anyone have an idea how to constrain this anion with Gromacs?
I checked mailing list archive but couldn't find any answer
corresponding to my question.
Without seeing a complete .mdp file, it's not possible to fully
diagnose this problem. The combination of SHAKE + particle
decomposition should be stable, but there are a whole host of different
things that can go wrong.
-Justin
Thanks in advance.
Gyorgy
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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title = BMIM PF6 bulk simulation
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS ;l_bfgs
integrator = md;steep
; Start time and timestep in ps
tinit = 0
dt = 0.00000001 ! just to see if it starts
nsteps = 25000
; mode for center of mass motion removal
comm-mode = linear
; number of steps for center of mass motion removal
nstcomm = 10
; group(s) for center of mass motion removal
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
;emtol = 50
;emstep = 0.5
;lincs_iter = 3
;lincs_warnangle = 50
; Frequency of steepest descents steps when doing CG
;nstcgsteep = 1000
;nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 10000
; Output frequency for energies to log file and energy file
nstlog = 10000
nstenergy = 10000
; Output frequency and precision for xtc file
nstxtcout = 10000
xtc-precision = 1000
; 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 =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 25
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.5
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME ; can RF also be used?
rcoulomb-switch = 0
rcoulomb = 1.5
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon_rf =
; Method for doing Van der Waals
vdw-type = Shift
; cut-off lengths
rvdw-switch = 1.1
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
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
; Temperature coupling
Tcoupl = V-rescale
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 1.0
ref_t = 298.15
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 4.0
compressibility = 4.5e-5 ; proper value for IL???
ref_p = 1.00
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
; annealing = no
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 298.15
gen_seed = 1993
; OPTIONS FOR BONDS
constraints = hbonds
constraint_algorithm = SHAKE
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