Dear all, Any idea please about my both questions below? The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule about c12 in either sections!
Thanks. Alex ---------- Forwarded message --------- From: Alex <alexanderwie...@gmail.com> Date: Tue, Sep 4, 2018 at 2:43 PM Subject: Adding new atom types To: <gmx-us...@gromacs.org> Hi all, Two questions on which your comments would be highly appreciated; 1. What is the difference between [ nonbond_params ] and [ pairtypes ] sections in ffnonbonded.itp file? For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have similar numbers for an the similar interactions when it is counted as [ nonbond_params ] or as [ pairtypes ] because of the scale = 1, but the "OE OA" interaction parameters change in [ nonbond_params ] to [ pairtypes ], similar story for the " OA O" interaction. Which is in contrast with my understanding of "fudgeLJ = 1". [ nonbond_params ] ; i j func c6 c12 * OE OA 1 2.261954E-03 1.505529E-06* * OA O 1 2.261954E-03 1.386510E-06* [ pairtypes ] ; i j func c6 c12 * OE OA 1 2.261954E-03 1.265625E-06* * OA O 1 2.261954E-03 9.687375E-07* 2. The gmx grompp gives some errors like; ERROR 1 [file topol.top, line xxxx] No default LJ-14 types Which needs me to introduce new atom type ( of the problematic atoms) in atomtypes.atp and then in ffnonbonded.itp; Would you please confirm the procedure I should take to do so; First I have to add the atom type in atomtypes.atp: OC24 is an example; *echo "OC24 15.99940" >> atomtypes.atp* Then: *Adding "OC24 8 15.99940 0.000000 A 0.0035644156892674973 6.222504156102231e-06" to the ffnonbonded.itp/[ atomtypes ]* Then: *Adding the "; i j func c6 c12" for the OC24 in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]* Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or the [ nonbond_params ] and [ pairtypes ] can be descided/governed by normal combination rule used in the FF, so that I do not need to put them in [ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] Thanks. Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.