Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happens to these 1-4 interactions at lambda=1 state?
Suppose 1 corresponds to CA and 4 corresponds to NA at state A (lambda = 0) and the CA_per and NA_per are the corresponding atomtypes at state B (lambda = 1). It is defined in the topology file that ... ... [ pairs ] 1 4 1 .... .... So does it mean that at state B (lambda = 1), the 1-4 nonbonded interactions will be calculated between CA_per and NA_per? Although the [ pairs_nb ] section is described in the manual, I would appreciate if someone elaborates a little more. -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5008996.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
