[gmx-users] Re: Adding a new water model to gromacs

[Justin Lemkul]

On 1/14/13 9:04 PM, learnmd wrote:
> Justin,
> Thanks for the direction.
>
> So, I have now edited spc template to create a new model called spchw.
>
> The spchw.itp for amber99 forcefield now looks like this:
>
> [ moleculetype ]
> ; molname nrexcl
> SOL 2
>
> [ atoms ]
> ; id  at type     res nr  res name  at name  cg nr  charge    mass
>    1   OW_spch      1       SOL       OW       1      -0.870   15.99940
>    2   HW_spch      1       SOL       HW1      1       0.435    2.00800
>    3   HW_spch      1       SOL       HW2      1       0.435    2.00800
>
> #ifndef FLEXIBLE
>
> [ settles ]
> ; OW funct doh dhh
> 1       1       0.1     0.16330
>
> [ exclusions ]
> 1 2 3
> 2 1 3
> 3 1 2
>
> #else
>
> [ bonds ]
> ; i     j       funct   length  force.c.
> 1       2       1       0.1     345000  0.1     345000
> 1       3       1       0.1     345000  0.1     345000
>
> [ angles ]
> ; i     j       k       funct   angle   force.c.
> 2       1       3       1       109.43  383     109.47  383
>
> #endif
>
> I have also edited the ffnonbonded.itp file for amber99 to include this
> model
>
>   atomtypes ]
> ; name      at.num  mass     charge ptype  sigma      epsilon
> Br          35      79.90    0.0000  A   0.00000e+00  0.00000e+00
> ; spch water - use only with spch.itp & settles
> OW_spch       8      15.9994  0.0000  A   3.16557e-01  6.50629e-01
> HW_spch       1       2.0080  0.0000  A   0.00000e+00  0.00000e+00
>
> Please advise if this is sufficient.
>

In principle.  Try it and see.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================