Hi Andrew! I've also been a bit confused by the names when I started looking at the force field definitions in GROMACS. Although Justin's replies contain all the information (as usual :)), let's try to shed some light with an example: consider a chain formed by atoms i-j-k-l-m-n; - means that there is a bond between atoms.
nrexcl specifies how many neighbors should be excluded when building lists of nonbonded interactions. nrexcl = 3 means that the first, second and third order neighbors (j, k and l for atom i; k, l and m for atom j; l, m and n for atom k; m and n for atom l; n for atom m) are excluded, such that the following pairs will be put on the lists to be passed to the nonbonded kernels: i m i n j n For another force field with nrexcl = 2, the following pairs would be passed to the nonbonded kernels: i l i m i n j m j n k n For another force field with nrexcl = 5, no pairs would be passed to the nonbonded kernels. More generally, any pairs which are neighbors of higher order than nrexcl will be put on the nonbonded lists. Parameters for these nonbonded interactions will be automatically computed from the topology data, based on the combination rules. If you have empty [bonds], [angles], [dihedrals] and [pairs] sections in the topology file, only the above interactions are considered for potential energy calculations. These nonbonded lists are dynamical and are remade based on neighbor search frequency; when using cutoffs, a pair whose atoms are further apart than the cutoff is not added to the list. Bonded interactions are specified in the [bonds], [angles] and [dihedrals] sections. Parameters for the bonded interactions are taken directly from the topology data after matching atom types. Any of these sections can be empty, if the force field is so designed; for OPLS-AA all these sections are present. There can be overlaps, f.e. if nrexcl = 2 and the topology file contains: [dihedrals] i j k l j k l m k l m n then atoms i and l, j and m and k and n will interact both as part of the dihedral angle potential and as nonbonded pair. Some force fields (like OPLS-AA) specify that the 1-4 interactions ((i l), (j m) and (k n) in the above example) should indeed be treated both as part of a dihedral angle potential and as nonbonded pairs; when treating them as nonbonded pairs there might be a scaling factor (0.5 for OPLS-AA). When there is no scaling factor (in other words, scaling factor is 1), a definition like above with nrexcl = 2 is all that is needed. For a scaling factor different from 1, the GROMACS implementation uses an explicit pairs list, called [pairs]. All 1-4 interactions should be included in the [pairs] section, which for the above example would look like: [pairs] i l j m k n It's the user's responsibility to add all needed (1-4 in case of OPLS-AA) pairs to the [pairs] section; pdb2gmx normally does this, but if you build the topology through other means then you have to make sure these pairs are generated. The interactions for these explicit pairs are always computed - even though they are computed through the nonbonded kernels, they are not subject to cutoffs. These explicit pairs also need parameters. The parameters are automatically generated when gen-pairs = yes from the topology data, based on the combination rules and the fudge (=scaling) factors. If gen-pairs = no, then the [pairs] section should contain both the atom indeces and the parameters. I found the name gen-pairs a bit misleading, I would have called it gen-pairs-params or something similar as it is only taken into consideration when looking for parameters; the [pairs] list is not automatically updated when generating the .tpr file. The [pairs] section offers some flexibility, as not only the 1-4 interactions but any other interaction that should be treated the same way can be included; a possible limitation is that only one fudge factor can be set for the whole list of explicit pairs. Care should be taken to not calculate the same interaction twice. With nrexcl = 3 and: [pairs] i m the nonbonded interaction between atoms i and m will be computed twice: once as part of explicit pairs list and once as part of nonbonded lists. Finally, I would like to point out that most of these can be found by reading the manual and experimenting with a toy molecular system (like the example above) using gmxdump and a combination of mdrun -rerun and g_energy. Cheers, Bogdan On Mon, Dec 10, 2012 at 9:13 PM, Andrew DeYoung <adeyo...@andrew.cmu.edu> wrote: > Javier and Mark, > > Thank you SO much! That is so helpful to me. > > If you have time, I have two follow-up questions: > > (1) From your answer, it seems that in OPLS, 1-4 interactions will be taken > into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified > in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are > provided in [ atomtypes ] in ffnonbonded.itp. > > But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a > protein for example? I think that in OPLS, such interactions are to be > considered at full strength (no scaling down). My question is: are these > 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions automatically taken > into account if gen-pairs = yes? > > (2) Suppose that I run grompp (where 1-4 interactions are specified in [ > pairs ] and gen-pairs = yes) and grompp gives me the following output: > > Generated 276 of the 276 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 276 of the 276 1-4 parameter combinations > > Does this output indeed imply that the ONLY nonbonded interactions > considered are 1-4 interactions? In other words, does this output suggest > that NO 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions are > considered? If so, why is this the case if I have set gen-pairs = yes? > > Andrew DeYoung > Carnegie Mellon University > > -- > 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. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
