Gromacs

Mixed Solvents

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    Version as of 00:40, 24 Aug 2019

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    A common question that new users have is how to create a system with mixed solvent (urea or DMSO at a given concentration in water, for example).  The simplest procedure for accomplishing this task is as follows:

    1. Determine the number of co-solvent molecules necessary, given the box dimensions of your system.
    2. Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro).
    3. Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box.
    4. Fill the remainder of the box with water (or whatever your other solvent is) using genbox.
    Page last modified 12:16, 13 Oct 2009 by JLemkul?