[gmx-users] How to obtain TIP4P/ε water model topology file

[Mark Abraham]

Hi,

Sorry, I can't do it for you. You can try asking the authors if they are
willing to share their tip4p.itp file, but otherwise you need to understand
how the paper the developed the mathematical model that used the parameters
it reports, and after reading the relevant parts of chapter 5 of the
GROMACS reference manual, see what values you need to transform and/or
replace in the modified form of tip4p.itp.

Mark

On Wed, Feb 21, 2018 at 8:16 AM Tushar Ranjan Moharana <
tusharranjanmoharana at gmail.com> wrote:

> Hi Mark,
> Thanks a lot for the suggestion. Just need a little more help. As per your
> suggestion I should edit the TIP3P topology. But the the forcefield
> (CHARMM36) has TIP4P.itp. Is there any advantage to edit  TIP3P.itp instead
> of TIP4P.itp. Also I don't know what to edit. According to the concerned
> paper, following are the parameter for different  water models. I want the
> last water model ( TIP4P/epsilon). But I couldn't find the values mentioned
> for the first one when I opened the TIP4P.itp (or TIP3P.itp).
>
> Table 1. Force Field Parameters of Non-Polarizable Water Models
> modelσ (Å)epsilon/*k*B (K)*q*H (e)*q*O (e)*l*OM (Å)μ (D)
> TIP4P 3.154 78 0.520 0.0 0.15 2.177
> TIP4P/2005 3.1589 93.2 0.5564 0.0 0.1546 2.305
> TIP4Q 3.1666 93.2 0.525 0.5 0.069 2.44
> TIP4P/epsilon 3.165 93.0 0.527 0.0 0.105 2.4345  It will be a great help if
> you can help me in modifying the same. Any tutorial or document will be
> absolutely fine. Following is how my TIP4P.itp looks like
>
>
> ;
> ; Note the strange order of atoms to make it faster in gromacs.
> ;
> [ moleculetype ]
> ; molname    nrexcl
> SOL        2
>
> [ atoms ]
> ; id    at type res nr    residu name at name cg nr    charge
> 1           OWT4           1       SOL        OW       1       0.0
> 2           HWT4           1       SOL       HW1       1       0.52
> 3           HWT4           1       SOL       HW2       1       0.52
> 4           MWT4           1       SOL        MW       1      -1.04
>
> #ifndef FLEXIBLE
> [ settles ]
> ; OW    funct    doh           dhh
> 1        1        0.09572    0.15139
> #else
> [ bonds ]
> ; i j    funct    length    force.c.
> 1    2    1    0.09572 502416.0 0.09572    502416.0
> 1    3    1    0.09572 502416.0 0.09572    502416.0
>
> [ angles ]
> ; i j    k    funct    angle    force.c.
> 2    1    3    1    104.52    628.02    104.52    628.02
> #endif
>
> [ exclusions ]
> 1    2    3    4
> 2    1    3    4
> 3    1    2    4
> 4    1    2    3
>
> ; The position of the virtual site is computed as follows:
> ;
> ;        O
> ;
> ;            D
> ;
> ;    H        H
> ;
> ; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
> ;      0.015 nm    / [ cos (52.26 deg) * 0.09572 nm    ]
>
> ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>
> [ virtual_sites3 ]
> ; Vsite from            funct    a        b
> 4    1    2    3    1    0.128012065 0.128012065
>
> Thanks a lot.
>
> On Wed, Feb 21, 2018 at 10:48 AM, Tushar Ranjan Moharana <
> tusharranjanmoharana at gmail.com> wrote:
>
> > Hi Henriques,
> > Thanks a lot for the suggestion. Actually it was TIP4P/(epsilon) which
> get
> > modified to TIP4P/?. I regret for the same. I completely agree with your
> > suggestion. Actually in an article (A fully atomistic computer simulation
> > study of cold denaturation of a β-hairpin) authors have shown that this
> > water model with CHARMM36 forcefield showed the best correlation with the
> > experiment. I went through the concern paper where the TIP4P/(epsilon)
> > model was tested (Non-Polarizable Force Field of Water Based on the
> > Dielectric Constant: TIP4P/ε). However I couldn't get the topology
> > (although parameters are mentioned). I have experimental data to verify
> if
> > the water model is not appropriate. It will be a great help if you can
> help
> > me getting/creating the topology.
> >
> > Thanks a lot for your suggestion.
> >
> > On Tue, Feb 20, 2018 at 10:00 PM, Tushar Ranjan Moharana <
> > tusharranjanmoharana at gmail.com> wrote:
> >
> >> Hi All,
> >> I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone
> >> let me know where can I get the corresponding .itp file.
> >>
> >> Thanks a lot.
> >>
> >> "A society with free knowledge is better than a society with free food"
> >> --
> >> Tushar Ranjan Moharana
> >> B. Tech, NIT Warangal
> >> Ph D Student, CCMB
> >>
> >
> >
> >
> > --
> > Tushar Ranjan Moharana
> > B. Tech, NIT Warangal
> > Ph D Student, CCMB
> >
>
>
>
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> --
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