[gmx-users] Re: angle constrain, constrained PF6 anion
Vitaly Chaban
vvchaban at gmail.com
Wed Feb 16 22:04:17 CET 2011
Hello,
I got your files. However, the error is completely another than you
mention and it occurs directly at the first time-step of the
simulation.
============================================
Inner product between old and new vector <= 0.0!
constraint #1 atoms 1377 and 1381
Wrote pdb files with previous and current coordinates
step 0Inner product between old and new vector <= 0.0!
constraint #1 atoms 2177 and 2181
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #1 atoms 2 and 6
Wrote pdb files with previous and current coordinates
Segmentation fault
============================================
There are a number of strange things in your configuration with the
unhealthy defined constraints in topology as probably the most severe
one. If you have constraints, why do you define bonds force constants
at the same time?
Good luck with your study,
Vitaly
On Wed, Feb 16, 2011 at 1:58 PM, <gyorgy.hantal at fc.up.pt> wrote:
>
> Hi Vitaly,
>
> Thanks for your answer. I was busy with other stuff these last two weeks,
> that's why I have time to reply only now.
>
> So the system is the BMIM PF6 ionic liquid.
> We chose two potentials to describe the system, and both treat the anion as
> rigid. We cannot use LINCS because it shouldn't be used if one constrains
> not only bonds but angles too, so we have to use SHAKE.
>
> But with SHAKE I encountered some strange things as I wrote in my first
> thread. In the attachement I am sending you all the files needed for the
> simulation, maybe you'll find the problem.
>
> I haven"t mentioned but we try to constrain the angles by adding fictious
> bonds. Maybe there is something wrong with this...
>
> Thank you in advance for your help.
>
> All the best,
> Gyorgy
>
>
> Quoting Vitaly Chaban <vvchaban at gmail.com>:
>
>> 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
>>
>
>
>
--
=========================
Dr. Vitaly V. Chaban, Ph.D.
Department of Chemistry
University of Rochester
Rochester, New York 14627-0216
The United States of America
=========================
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