On Thu, Aug 15, 2013 at 12:04 AM, Christopher Neale <chris.ne...@mail.utoronto.ca> wrote: > >From my inspection of the force field files included in gromacs-4.6.1, when > >you > use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen type > HT, > which does have LJ on the hydrogen atoms, whereas you only get the hydrogen > type HWT3 when you use the non-charmm tip3p (tip3p.itp). > > If I understand Mark's comment to be that there is no good reason to use the > charmm > tip3p water model with the charmm ff, then I disagree (See below). > > I have posted an image ( http://tinypic.com/r/110ak5s/5 ) of the area per > lipid (APL) > for a POPC bilayer that I built with charmm-gui (83 lipids/leaflet; 43 > waters/lipid) > and then simulated under the charmm36 lipid parameters for ~ 300 ns many times > successively with different water models (2 repeats each, starting from > different > conformations out of charmm-gui). Note the large difference in the APL for the > regular tip3p and the charmm tip3p. In fact, some papers note that you get > gel-phase bilayers with the charmm36 lipid ff and the non-charmm tip3p model > when using > certain cutoff treatments > (Piggot and Khalid -- http://pubs.acs.org/doi/abs/10.1021/ct3003157 -- is one > such paper).
Good to know, thanks! Mark > Chris. > > -- original message -- > > You could do that, but it's extra cost for no known benefit. See > http://dx.doi.org/10.1021/ct900549r > > On Tue, Aug 13, 2013 at 7:15 PM, Weilong Zhao <wz24 at zips.uakron.edu> wrote: >> Hi, >> >> I noticed that for GROMACS versions of 4.5 of later, the force field for >> TIP3P water model in CHARMM27.ff package has a following line included: >> >> The following atom types are NOT part of the CHARMM distribution >> .. >> . >> HWT3 1 1.008000 0.417 A 0.0 0.0 ; TIP3p H >> >> It seems that VDW interaction of the default hydrogen of water is switched >> off, which makes it not the correct TIP3P ff of CHARMM. However this >> hydrogen type HWT3, is used as default by gromacs as CHARMM water model. >> >> Even though the hydrogen without VDW is the original TIP3P water model, I >> wonder is there any problem to include it in CHARMM ff set? Really >> appreciate if anyone could share some opinion. > -- > 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
