Thanks Justin. I was just making sure that I was modifying the relevant files. On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Sai Pooja wrote: > >> When using the charmm forcefield, the following is the case: >> 1. ffnonbonded.itp - has listed paramters for tip3p (and other water >> models) OWT3 and HWT3 >> 2. ffbonded.itp - does not have paramters for OWT3 and HWT3 >> Does this mean: >> 1. nonbonded parameters for tip3p are read from ffnonbonded.itp for ALL >> nonbonded interactions OR >> for water-water interactions are read from tip3p.itp file and for >> protein-water are read from ffnonbonded.itp? >> >> > > Nonbonded interactions are applied uniformly, unless they are modified in a > specific [nonbond_params] directive. Isn't this something we've worked > through before? > > http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html > > > 2.bonded paramters for tip3p are read from tip3p.itp file? >> >> > > Bonded parameters for water models are really only relevant if using a > flexible model (which you shouldn't). Otherwise, the SETTLE algorithm > simply fixes the geometry. This is all determined by the #ifdef FLEXIBLE > statement in, for instance, tip3p.itp. > > -Justin > > > Pooja >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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