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

learnmd joinforfun8909 at gmail.com
Sun Jan 13 19:57:31 CET 2013


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
Deuterium and still count it as hydrogen bond or should I just use H in the
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

I am using Gromacs 4.5.5

Thanks for taking the time to help me out. 

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