[gmx-users] Re: angle constrain, constrained PF6 anion

[Vitaly Chaban]

Hey  Gyorgy,

Your current topology file(s) is(are) also important to analyze the
situation and fix the problem.

Pass my kind regards to Julia...

========================
Dr. Vitaly V. Chaban, Ph.D.
Department of Chemistry
University of Rochester
Rochester, New York 14627-0216
The United States of America
=========================


> 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