[gmx-users] How to use/obtain TIP4P-D water model?

Andrew Guy andrew.guy at burnet.edu.au
Wed Sep 14 05:22:40 CEST 2016


Dear João,

Many thanks for the detailed response. I have emailed you regards your
custom AMBER ff99SB-ILDN modified for use with TIP4P-D, as this would be
very helpful.

Kind regards,

Andrew

Message: 1
> Date: Tue, 13 Sep 2016 09:22:58 +0200
> From: Jo?o Henriques <joao.henriques.32353 at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] How to use/obtain TIP4P-D water model?
> Message-ID:
>         <CALC+HGQjBiGzDW+xjQVeZfKDDyoLdSUT218aOD3R30+
> nARAwkg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Andrew,
>
> [1] From Stefano Piana's own words:
>
> "The parameters of the model are reported in Table 1 of the paper (charge
> on the hydrogen 0.58, C6=900 kcal/mol/A^6 C12=904657 kcal/mol/A^12). The
> geometry is the same as the TIP4P/2005 water model of Vega and Miguel. To
> run simulation with TIP4P-D in GROMACS, you may use the TIP4P/2005 water
> model as a starting point and modify the charges and LJ parameters."
>
> - - -
>
> [2] In more technical "GROMACS terms", this is the procedure:
>
> You need to add the new oxygen atom type for TIP4P-D along with its C6 and
> C12 parameters into your "ffnonbonded.itp". Notice that you need to convert
> Piana's parameters into the right units for GROMACS. Then, you need to
> create an individual topology for TIP4P-D. I used the topology of the
> TIP4P/2005 model from Abascal et al. as the base and changed the partial
> charges and atom types. If you can't find the TIP4P/2005 topology, use the
> "TIP4P.itp" which is included in most force field directories, but be aware
> that the virtual sites parameters differ slightly. Make sure the atom types
> check with the new entries under "ffnonbonded.itp". To end, add an entry
> for the new water model under "watermodels.dat", so that you get presented
> with the option to select that water model when you run "pdb2gmx".
>
> One extra note, you need to solvate the system using an appropriate
> pre-equilibrated water box that fits with this model.
>
> - - -
>
> [3] I have never used GROMACS 2016, so a lot of this stuff may change or
> not. I am not familiar with the changes. Maybe one of the experts on this
> list can help you with that. What I can do is provide you with my own
> custom AMBER ff99SB-ILDN modified for use with TIP4P-D, but it is intended
> to be used for GROMACS 4.6.7.
>
> Best regards,
> Jo?o
>
>
>
>
> On Tue, Sep 13, 2016 at 4:15 AM, Andrew Guy <andrew.guy at burnet.edu.au>
> wrote:
>
> > Hi all,
> >
> > I am trying to follow the approach used by Henriques and Skep? (2016) to
> > model a short disordered protein region (
> > http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00429).
> >
> > In their paper, they use GROMACS with a new water model, TIP4P-D. I am
> > unsure how to go about adding and using this water model in GROMACS.
> >
> > I suspect I have to add a new water model in my gromacs/share/top folder,
> > or perhaps in the relevant subfolder for the force field I am using.
> > However, I only have the parameters for TIP4P-D that are listed in the
> > primary reference - http://pubs.acs.org/doi/suppl/10.1021/jp508971m -
> and
> > don't know how to translate these to a format suitable for GROMACS. I
> have
> > also tried reading through the GROMACS manual, but couldn't seem to find
> > anything.
> >
> > Many thanks,
> >
> > Andrew
> >
> > (p.s. I am using GROMACS 2016)
> > --
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