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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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