[gmx-users] angle constrain, constrained PF6 anion
gyorgy.hantal at fc.up.pt
gyorgy.hantal at fc.up.pt
Tue Feb 1 19:47:11 CET 2011
The mdp file is attached.
Best,
Gyorgy
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> gyorgy.hantal at 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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-------------- next part --------------
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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