[gmx-users] hints for core/shell optimization?

[Tamas Karpati]

Dear Justin,

Thank you for your quick answer.

Same with GROMACS-4.6.6: core-to-shell distance
must be >0 to not crash. My crystal is expected to be polarized
(metallic and oxygen sites are the victims of this model).
The *.mpd file being used is:

#   nstcalcenergy = 1 ; 4.6.6 claims this necessary, 4.6.3 didn't need it
#   integrator      = steep
#   vdw-type        = cut-off
#   coulombtype     = pme
#   nsteps          = 10
#   periodic-molecules = no
#   cutoff-scheme = group
#   ns-type = grid
#   emtol = 10 ; default=10 kJ/mol/nm
#   niter = 10000 ; default=20
#   ;fcstep = ; default=0 ps^2 ; not quite clear what it is
#   rlist           = 1.0
#   rcoulomb        = 1.0
#   rvdw            = 1.0
#   pbc             = xyz
#   nstxout = 1  ; wouldn't emit pos for each, though
#   nstfout = 1 ; -"-
#   nstlist = 1000 ; avoid it, no bonds at all
#   nstlog  = 1
#   ;pcoupl = no ; used to switch cell-optimization on/off

Best regards,
  toma

On Fri, Jul 25, 2014 at 1:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/25/14, 7:43 AM, Tamas Karpati wrote:
>>
>> Dear all,
>>
>> I have two questions about geometry optimization of a crystal
>> with polarization via the core/shell model. I'm creating *.gro and
>> *.top files "by hand" and compile them with *.mdp to *.tpr via
>> GROMPP. My FF is also made by hand (simply because i need
>> to learn GROMACS). I have learnt on this list that with Buckingham
>> potentials I need to use the group rather than the Verlet scheme.
>>
>>
>> (1/2) Letting some of all atoms be polarizable through applying
>> shell particles made MDRUN segfault like this:
>>
>> #  ...
>> #  Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision)
>> #  Using 2 MPI threads
>> #
>> #  Steepest Descents:
>> #     Tolerance (Fmax)   =  1.00000e+01
>> #    Number of steps    =           10
>> #  Segmentation fault1.0e-02 nm, Epot=         -nan Fmax= 3.76506e+03,
>> atom= 1357
>>
>> I imagined some divison by zero situation not handled and have put
>> some "random noise" on the shell particles' position so they do not
>> anymore start exactly at the atomic sites (meaning nonzero distances).
>> Seemed to work, at least no further crashes. Only energies and forces
>> seem very high:
>>
>> #  Steepest Descents:
>> #     Tolerance (Fmax)   =  1.00000e+01
>> #     Number of steps    =           10
>> #  Step=    0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05,
>> atom= 160
>> #  Step=    1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06,
>> atom= 160
>> #  Step=    2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08,
>> atom= 2759
>> #  Step=    3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09,
>> atom= 468
>> #  Step=    8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09,
>> atom= 1095
>> #  Step=   10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08,
>> atom= 1096
>> #  Energy minimization reached the maximum numberof steps before the
>> forces
>> #  reached the requestedprecision Fmax < 10.
>>
>> My question is the following.
>>     Is it (randomized shell positions) a correct procedure with GROMACS?
>>
>>
>> (2/2) Changing from a randomized x/y/z set to a fixed distance at
>> a random direction for the shell particles led to another unexpected
>> result.
>> I scanned a range between 1e-4 to 0.1 nm and noticed that
>>
>>      the final core-to-shell distance is a function of the starting one.
>>
>> I used niter = 10000 (note: the default is 20) as i noticed in an MD
>> type of job that 20, 100 or 1000 steps were insufficient for the shells
>> to relax within default tolerance. The cell size was ca. 3x3x3 nm.
>>
>
> Please provide a full .mdp file; other settings are very relevant.
>
>
>> My question is the following.
>>     What would be the appropriate core-to-shell distance to apply?
>>
>
> The equilibrium distance for core-shell bonds should be zero, deviations
> from this non-polarized state account for the polarization energy.
>
>
>> I appreciate any help so thanks in advance.
>
>
> Upgrade to 4.6.6; there have been issues with shells that have been fixed
> since 4.6.3.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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