# [gmx-users] Some notes on parameterising dreiding

Tue Nov 20 18:29:25 CET 2012

```It took me quite a while to get to grips with this and, since the question was asked about a year ago by someone else with no response, I thought I'd share my insight.

LJ potentials:  Its important to note the slight difference from the widely used form. You need to convert Ro to sigma by dividing by 2^(1/6) (see wikipedia on the LJ interaction). I've also found that although the paper states that you can either include, exclude or scale the LJ 1-4 interactions I've found it work best to exclude them. As far as I can tell this means setting nrexcl to 4 in your topology.

Bond stretch: This is a straightforward harmonic potential (type 1 in gromacs). All you need to do is convert the length from A to nm and the force constant from kcal/mol/A^2 to kJ/mol/nm^2 by multiplying by 4.184/0.01

Angles: Although the paper states that the cosine harmonic (type 2 in gormacs) is preferred I've seen this generate some unstable systems. Both the paper and the gromacs manual tell you how to convert to the normal harmonic form (type 1 in gromacs). Just convert the force constant from kcal/mol/rad^2 to kJ/mol/rad^2. Leave the angles as degrees.

Dihedrals: There is already a thread on here about this and the conversion does work (search for dihedral form) for methanol at least. Just remember to convert from kcal to kJ. The force constant for resonant bonds seems to be too high though (the paper gives 25 kcal/mol which converts to 25*4.184*0.5=52.3 again see previous posting for the conversion) but a force constant of 40 seems to result in a stable system. Higher values may work but I've not tested them yet. Its possible that including some improper dihedrals (inversions in the dreiding paper) may fix this but its not been tested.

If anyone has any coments on why this force constant seems unacceptable I'd like to hear it!

I'm still testing this out so if the system may still blow up but this is a good start for anyone trying to parameterise dreiding. I hope this helps someone.

Below is the force field file that I've generated for my system. The atoms names follow the opls convention since I originally simulated this system with opls-aa and it would have taken extra effort to change all my topologies (I have some complicated molecules). I would advise someone starting from scratch to stick with the dreiding naming convention, edit this (if you're using it) and check for any double entries that may occur e.g. HC should be exactly the same as HA resulting in the same line twice under [ atomtypes ] so one of them can be removed.

-------------------------------------------------------------

[ defaults ]
; nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
1            3            yes        1        1

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name      bond_type    mass        charge       ptype    sigma      epsilon
opls_135   CT    6     12.01100    -0.180       A    3.47299e-01  3.97898e-01
opls_136   CT    6     12.01100    -0.120       A    3.47299e-01  3.97898e-01
opls_137   CT    6     12.01100    -0.060       A    3.47299e-01  3.97898e-01
opls_140   HC    1      1.00800     0.060       A    2.84642e-01  6.35968e-02
opls_145   CA    6     12.01100    -0.115       A    3.47299e-01  3.97898e-01
opls_146   HA    1      1.00800     0.115       A    2.84642e-01  6.35968e-02
opls_186   OS  8     15.99940    -0.400       A    3.03315e-01  4.00409e-01
opls_260   CA  6     12.01100     0.035       A    3.47299e-01  3.97898e-01
opls_902   NT  7     14.00670    -0.630       A    3.26256e-01  3.23842e-01
opls_154   OH  8     15.99940    -0.683       A    3.03315e-01  4.00409e-01 ; methanol
opls_155   HO  1      1.00800     0.418       A    2.84642e-01  6.35968e-02 ; methanol
opls_156   HC  1      1.00800     0.040       A    2.84642e-01  6.35968e-02 ; methanol
opls_157   CT  6     12.01100     0.145       A    3.47299e-01  3.97898e-01 ; methanol

[ bondtypes ]
; i      j    func      b0      kb
CA    CT      1    0.14600   292880.0
CT    HC      1    0.10900   292880.0
CA    CA      1    0.13900   439320.0
CA    NT      1    0.13920   292880.0
CT    NT      1    0.14620   292880.0
CA    HA      1    0.10200   292880.0
CA    OS      1    0.13500   292880.0
CT    CT      1    0.15300   292880.0
OH    HO      1    0.09800   292880.0  ; methanol
OH    CT      1    0.14200   292880.0  ; methanol

[ pairtypes ]

[ constrainttypes ]

[ angletypes ]
;  i       j      k    func     th0       cth
HC      CT     CT       1   109.471    418.400
HC      CT     NT       1   109.471    418.400
NT      CT     NT       1   109.471    418.400
CT      CT     CT       1   109.471    418.400
HC      CT     CA       1   109.471    418.400
CA      CT     CA       1   109.471    418.400
NT      CT     CA       1   109.471    418.400
CA      CA     CA       1   120.000    418.400
HA      CA     CA       1   120.000    418.400
HA      CA     CT       1   120.000    418.400
CA      CA     CT       1   120.000    418.400
CA      CA     NT       1   120.000    418.400
CT      CA     NT       1   120.000    418.400
HA      CA     NT       1   120.000    418.400
CA      NT     CT       1   106.700    418.400
CT      NT     CT       1   106.700    418.400
CA      OS     CA       1   104.510    418.400
HO      OH     CT       1   104.510    418.400 ;methanol
OH      CT     HC       1   109.471    418.400 ;methanol
HC      CT     HC       1   109.471    418.400 ;methanol

HC      CT     CT       2   109.471    470.741
HC      CT     NT       2   109.471    470.741
NT      CT     NT       2   109.471    470.741
CT      CT     CT       2   109.471    470.741
HC      CT     CA       2   109.471    470.741
CA      CT     CA       2   109.471    470.741
NT      CT     CA       2   109.471    470.741
CA      CA     CA       2   120.000    557.956
HA      CA     CA       2   120.000    557.956
HA      CA     CT       2   120.000    557.956
CA      CA     CT       2   120.000    557.956
CA      CA     NT       2   120.000    557.956
CT      CA     NT       2   120.000    557.956
HA      CA     NT       2   120.000    557.956
CA      NT     CT       2   106.700    456.093
CT      NT     CT       2   106.700    456.093
CA      OS     CA       2   104.510    446.452
HO      OH     CT       2   104.510    446.452 ;methanol
OH      CT     HC       2   109.471    470.741 ;methanol
HC      CT     HC       2   109.471    470.741 ;methanol

[ dihedraltypes ]
; i    j    k    l   func   phi0     cp     mult
CA   CA   CT   X    1     180.0   2.092    6
X    CT   CA   X    1       0.0   4.184    3
X    CT   CT   X    1       0.0   4.184    3
X    CT   NT   X    1       0.0   4.184    3
X    CA   NT   X    1       0.0   4.184    3
CA   CA   NT   X    1     180.0   2.092    6
X    CA   CA   X    1        180.0   40.30    2
X    OS   CA   X    1     180.0   4.184    2
X    OH   CT   X    1       0.0   4.184    3  ;methanol

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