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

[Tushar Ranjan Moharana]

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