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

[learnmd]

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.

Thanks







On Sun, Jan 13, 2013 at 2:02 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5004528h28 at n6.nabble.com> wrote:

>
>
> On 1/13/13 1:57 PM, learnmd wrote:
> > Hello,
> >
> > I am new to gromacs and I hope I can get help with a problem. I want to
> add
> > a heavy water model to gromacs and then run simulations with a box full
> of
> > that solvent. I know the parameters (the O-D) bond length, bond angles
> and
> > LJ parameters for the system.
> >
> > How do I make an .itp file for this system? Will Gromacs recognize D as
>
> Write it in a text editor after a thorough read through Chapter 5 of the
> manual.
>   You can edit an existing file (like spc.itp) if you want a template.  If
> you're introducing new atomtypes and other parameters, you will need
> additional
> directives (again, consult Chapter 5).
>
> > Deuterium and still count it as hydrogen bond or should I just use H in
> the
>
> There's nothing during run time that cares about hydrogen bonds.  The
> g_hbond
> program determines putative hydrogen bonds by reading atom names.  In that
> case,
> using the name "H" is useful, but a topology can be hacked afterwards to
> use
> whatever atom names you like.
>
> > model to avoid such confusion. Also, how do I make an initial coordinate
> > file and then a box of solvent (like the spc216.gro) provided in the
> > installation.
> >
>
> genbox -ci -nmol or simply use spc216.gro and equilibrate thoroughly, as
> is done
> with other 3-point models.
>
> -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
>
> ========================================
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