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

Justin Lemkul jalemkul at vt.edu
Sun Jan 13 20:01:06 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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