Water modeling problems

Hi all,
Greetings.
I’m new to Lammps and I really have a brunch of questions to ask, hope you can kindly help this poor green hand.
Here are the first two quest:

1.How do you generally create a water model, or the data file?
Unlike the metals, some of which are often defined in in-files, water simulation seems to need a data file. And so far all my data files are downloaded from the Internet and revised by a python script to meet my need. But this is pretty troublesome. I hope to find a way to easily create a water model (like I only need to put in some parameters and the size of the model)

2.How is the hydrogen bond defined or calculated in Lammps? And how can I count the total amount of the hydrogen bond?
In the data file, TIP3P or TIP4P or other models, there is no hydrogen bond defined. So I’m wondering whether the hydrogen bond is calculated automatically during the operation?But I haven’t seen any tips or introductions about hydrogen bond from the COMMANDS website. Or, do I have to use another software to count/calculate hydrogen bond? But there is no information about hydrogen bond in the dump/log file either…I am simulating the melting and icing duration of water/ice , so I really want to know about the hydrogen bond.

Hope someone can answer my questions.
Many thanks.

sincerely,

Denzel

  1. You can use Solvate tool in VMD or Moltemplate tool for making water molecules. There may be some other options as well, like using software such as Materials Studio, HyperChem, arguslab and etc. You may check Pre/Post Processing Tools for use with LAMMPS page as well.

  2. There is a command related to H-bonds in lammps. Please check this page: pair_style hbond/dreiding/lj command.
    You can use Hydrogen bond analysis tool in VMD to calculate the number of H-bonds between different residues.

Hope these help.