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JOYCE Tutorial. Part (I / III)

Author: Anna Piras, Pablo M. Martinez

Contact: anna.piras@pi.iccom.cnr.it

Keywords: Tutorial, FF, JOYCE

Welcome to the introductory JOYCE tutorial. Here, we will discuss the fundamentals of JOYCE and learn how to get set to build our own force fields (FF) for a simple rigid molecule. Part II will cover the fitting of stiff internal coordinates while part III will revolve around the validation of the force field.

Our sample molecule and atom assignation

We will be developing a FF for the pyridine molecule. It is a simple aromatic system, useful as a first example.

Alt text

We should first decide how many chemically distinct atoms conform the molecule. This is usually assessed through symmetry arguments.

Alt text

The assigned names are:

  • N for the nitrogen atom
  • C1 for the carbon atoms in orto position
  • H1 for the hydrogen connected to the carbon atoms in orto position
  • C2 for the carbon atoms in meta position
  • H2 for the hydrogen connected to the carbon atoms in meta position
  • C3 for the carbon atoms in para position
  • H3 for the hydrogen connected to the carbon atoms in para position

QM data

JOYCE fits the force field on quantum-mechanical information. In the case of pyridine, the only data necessary is the hessian, that can be computed with a variety of softwares, such as Gaussian and Orca. Here, no details on how to perform the QM computations will be provided; instructions and details can be found on the website of the selected software (see here for a selection). Once the computation is performed, a formatted file (.fcc or .fchk) containing the relevant information must be created. In this case, the obtained .fcc file is:

INFO
State file generated

GEOM      UNITS=ANGS
    11
Geometry from pyridine.opt+freq.fchk in xyz format (with filter: all)
N        0.11422238   0.00436653   1.42368457
C        0.09245599   1.14861478   0.72599345
C        0.04820438   1.21011127  -0.67045418
C        0.02582116   0.01272872  -1.38799711
C        0.04884050  -1.18910531  -0.67711800
C        0.09198441  -1.13601766   0.71935087
H        0.11104643   2.07093040   1.31705188
H        0.03198657   2.17644748  -1.17898424
H       -0.00867702   0.01563431  -2.48017998
H        0.03314471  -2.15214043  -1.19180578
H        0.11097050  -2.06157010   1.30536078

ENER      UNITS=AU
 -2.48299537E+02

GRAD      UNITS=AU
  1.83034402E-05  1.81651764E-05  4.11559030E-05  4.80832521E-05  8.29667173E-06
  7.54249850E-05 -6.22267303E-06 -2.58765830E-05 -1.74854528E-04 -3.81225122E-05
  2.05939890E-04 -1.11341585E-05  1.07479629E-04 -1.38157910E-04  1.71489384E-04
 -1.56118706E-04 -1.02156512E-04 -1.22322162E-04 -1.13877674E-05  1.15999532E-05
 -1.70632155E-05  5.90267247E-06  1.61592947E-05  2.37764591E-05 -1.28615069E-05
 -7.72129738E-06 -1.96723105E-05  6.96854131E-06  2.72662105E-05  6.20796475E-06
  3.79756311E-05 -1.35148944E-05  2.69916786E-05

HESS      UNITS=AU
  9.47745045E-02  3.73392890E-05  6.52781439E-01  9.85074334E-03  5.04961677E-04
  4.07847691E-01 -6.74401191E-02  2.64937251E-03 -3.68275736E-03  1.58513284E-01
  3.51554284E-03 -2.82463990E-01  1.12371936E-01  1.45386614E-03  7.28522647E-01
 -3.70370330E-03  8.37724074E-02 -1.85053925E-01  1.67249601E-02  4.63921313E-02
  6.89254734E-01  2.34701771E-02  3.12556170E-03 -1.60845313E-03 -7.03237348E-02
 -1.13821423E-03 -8.12672438E-03  1.31693065E-01  1.10798365E-03  2.77066669E-02
  3.51678189E-02  1.15069047E-03 -1.32844158E-01  3.55806982E-02 -1.07354916E-03
  7.40977629E-01 -1.58415148E-03  9.96248682E-02 -2.71683518E-02 -8.15135518E-03
 -3.66312649E-02 -3.28607465E-01  1.71914192E-02 -3.09264695E-02  6.76829468E-01
 -1.03315089E-02  1.74561701E-05  4.68369171E-04  8.30646572E-03 -9.92126433E-04
 -1.11776330E-03 -6.35153112E-02 -4.09190100E-03 -3.91253579E-03  1.42024425E-01
 -2.44891528E-05 -8.27113579E-02 -2.44945682E-04 -2.54677139E-03  4.31225495E-02
 -8.10450900E-02 -2.04305622E-03 -2.91331152E-01 -6.60212768E-02 -1.82999075E-04
  6.71003325E-01  4.63561899E-04 -2.43893980E-04  4.58121425E-03 -1.12598175E-03
 -3.03515183E-02 -2.77787320E-02 -3.89829452E-03 -1.31484954E-01 -1.88051296E-01
  1.92285530E-02  3.25896491E-04  7.51093351E-01  2.34524018E-02 -3.13042488E-03
 -1.63089375E-03 -1.01444126E-02  1.27923396E-03 -1.51974166E-03  6.18309384E-03
  6.62403683E-04  1.97982565E-03 -6.35978700E-02  2.17550450E-03 -3.93208029E-03
  1.31693083E-01 -1.07451225E-03  2.84668348E-02 -3.48605363E-02  7.97396038E-04
 -1.81081252E-02  2.49758042E-02 -6.52892324E-04 -5.58028753E-02 -2.16075006E-02
  4.23792873E-03 -2.91685660E-01  1.30420553E-01  7.06758075E-04  7.39787911E-01
 -1.59147659E-03 -9.93230990E-02 -2.79641401E-02 -1.52294036E-03  4.07204413E-02
 -5.82104240E-02  1.98747846E-03  2.08900892E-02  6.89711777E-02 -3.94346736E-03
  6.49334724E-02 -1.86685445E-01  1.69662297E-02  3.18923078E-02  6.78032511E-01
 -6.74625940E-02 -2.66948433E-03 -3.71922681E-03  2.65305473E-03 -8.01088637E-04
  1.86737185E-03 -1.01512536E-02 -7.85036332E-04 -1.52168408E-03  8.30435790E-03
  2.55932524E-03 -1.13206732E-03 -7.02382372E-02 -1.08845795E-03 -7.95858011E-03
  1.58465673E-01 -3.56203019E-03 -2.80984240E-01 -1.12728213E-01  7.80322929E-04
 -9.82933294E-02  2.61058505E-02 -1.28192304E-03 -1.77165877E-02 -4.04735931E-02
  9.64294073E-04  4.24696627E-02  3.07323272E-02  1.20757166E-03 -1.32864065E-01
  3.77823028E-02 -1.59106809E-03  7.28611420E-01 -3.77313047E-03 -8.41161459E-02
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  6.89507662E-01 -4.20723759E-03  5.61005598E-04  5.65293853E-04 -4.16266435E-02
 -4.06774316E-03 -3.32054302E-03  6.55413040E-03 -8.51242416E-04 -5.48996460E-04
  7.16375910E-03  5.60464009E-05 -4.12677812E-04 -5.56103566E-04  3.38779634E-05
  5.88509230E-06  1.07600607E-02  1.54230368E-04 -3.16948059E-04  2.66844689E-02
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  7.99365143E-05 -1.74486141E-03  2.49870808E-03  4.13513547E-03  2.65348145E-01
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 -3.23462701E-04  4.81768907E-03  4.54451286E-04  3.86294305E-03  1.30780793E-01
  1.48517038E-01  8.04122665E-03  2.69601998E-05 -4.77345107E-04  9.32570614E-04
  9.55079005E-04 -2.01818077E-04 -3.63511361E-02  3.68715511E-03 -2.66543931E-03
  2.76677211E-03 -4.86451783E-04  2.74756291E-04  8.07451390E-03 -1.07371494E-04
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 -1.51934359E-05  1.21232760E-04  2.55249774E-02  1.11976424E-05  1.89627538E-03
  3.07644813E-04 -9.37679383E-05  1.82127968E-03 -2.94176597E-03  3.70052360E-03
 -2.77510507E-01  1.16446735E-01  4.93965336E-04 -1.73997195E-02  1.54896298E-02
 -1.34077538E-04 -2.55067137E-03 -4.29080828E-03 -3.00208496E-05  3.02812983E-04
 -9.70003179E-04  1.14213198E-05  5.00277590E-04  3.93651657E-04 -3.98586523E-03
  2.92644498E-01 -4.73213440E-04  6.67078223E-04 -6.96159492E-03 -2.07416793E-04
  3.00244979E-02 -5.65372924E-03 -2.66930239E-03  1.16376773E-01 -1.19834202E-01
  2.77418056E-04 -1.57799520E-02  1.14498652E-02 -2.81166985E-04 -3.43325648E-03
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  8.29137796E-05 -4.93293775E-03  2.38376845E-03 -4.56538556E-05  1.01713802E-04
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  2.30637499E-04 -7.01590039E-04  1.58191844E-04 -1.19792294E-04  9.40565564E-04
  1.04192970E-02 -7.98017768E-04  3.57148922E-01  8.05183416E-03 -2.48801955E-05
 -4.66913002E-04 -3.42738946E-04  6.20037979E-05 -3.32787749E-05  8.06440442E-03
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  2.85914717E-04  9.80709622E-04  1.42305469E-04 -2.60078321E-03  4.28110776E-03
 -4.87431943E-04 -1.74135968E-02 -1.56617909E-02 -3.55510104E-03 -2.76080059E-01
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  3.82348438E-06 -1.13073690E-04 -2.68073503E-05 -8.06033833E-04 -8.54128574E-04
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  4.25877740E-05 -1.05054328E-05 -3.08805313E-03 -1.29783325E-05  1.19642164E-04
  2.66943727E-02  2.15454920E-04 -3.29776549E-02  6.68838693E-03 -7.46873863E-05
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 -7.68526403E-06  9.50063371E-05 -2.25920052E-04  1.18658686E-05  4.99158271E-04
  4.51499657E-04 -4.22373701E-03  2.66765781E-01  5.64246379E-04 -1.84989030E-02
  1.35824572E-02 -3.26893587E-04 -4.83203476E-03  4.11878564E-04  8.74617442E-06
 -1.01395553E-03 -3.14224396E-04 -4.02288697E-04 -1.64784789E-03 -5.74398270E-03
 -5.65573710E-04  2.69812995E-02 -1.07996402E-02 -3.31969679E-03  1.28559624E-01
 -1.44660107E-01 -7.74912562E-06 -5.89666991E-04  3.04981873E-04  6.40381010E-05
  1.12653340E-04  1.48572882E-04 -1.22218833E-05  1.42693547E-03 -6.94226334E-04
  1.20965277E-04 -3.95431887E-04  7.08319891E-04  3.87642787E-03 -1.30102672E-01
  1.47055971E-01

Continue with the tutorial here to start the fitting procedure.