An important final point is that you can always see EXACTLY what grompp is putting into the B state by running gmxdump on the resulting tpr. It's a LOT of information, but all in text all the interactions are listed explicitly there.
On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/10/13 2:50 PM, JW Gibbs wrote: >> >> 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. >> > > The actual answer depends on exactly how you're treating the system. Are > you using [pairs_nb] in your topology or just [pairs]? The outcome will be > different depending on which you're using. Also note that, as the manual > says, you don't really need to mess with [pairs_nb] at all; you can achieve > unscaled internal interactions using "couple-intramol = no" in the .mdp > file. Without seeing the .mdp file, it's even more difficult to know what > you're doing and what you should expect. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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
