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

[João Henriques]

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,
João




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 Skepö (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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