On 3/31/20 12:59 PM, Andrey Gurtovenko wrote:
Dear All, Recently I realized that I don't fully understand what should be done in Gromacs to account for 1-4 LJ interactions. According to the manual: "gen-pairs is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting ‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ." http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html Therefore, I had an impression that to account for 1-4 interactions in some generic force-field, it is enough to set gen-pairs=yes. However, it turns out that this is not the case: in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the [pairs] section of the topology file of a system. Otherwise 1-4 interactions are NOT accounted for. Can someone comment on this? If I am right, maybe it is worth to clarify this point in the manual?
The language in the manual is correct, either pair *parameters* are generated, or they are not. The topology is different from the parameters; if *interactions* are not there, then nothing is done.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
