Water Solvation

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    When using genbox to generate a box of solvent, you need to supply a pre-equilibrated box of a suitable solvent for genbox to stack around your solute(s), and then to truncate to give the simulation volume you desire. When using any 3-point model (e.g. SPC, SPC/E or TIP3P) you should specify -cs spc216.gro which will take this file from the gromacs/share/top directory. Other water models (e.g. TIP4P and TIP5P) are available as well. Check the contents of the /share/top subdirectory of your GROMACS installation. After solvation, you should then be sure to equilibrate for at least 5-10ps at the desired temperature. You will need to select the right water model in your .top file, either with the -water flag to pdb2gmx, or by editing your .top file appropriately by hand.

    For information about how to use solvents other than pure water, please see Non-Water Solvation or Mixed Solvents.

    Page last modified 12:08, 13 Oct 2009 by JLemkul?