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 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 installation. I am using Gromacs 4.5.5 Thanks for taking the time to help me out. -- View this message in context: http://gromacs.5086.n6.nabble.com/Adding-a-new-water-model-to-gromacs-tp5004527.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
