Gromacs

Non-Water Solvation

    It is possible to use solvents other than water in GROMACS.  The only requirements are that you have a pre-equilibrated box of whatever solvent you need, and suitable parameters for this species in a simulation.  One can then pass the solvent box to the -cs switch of genbox to accomplish solvation.  One problem that new users encounter is that they expect their topology to be automatically updated if it was fed to the -p switch of genbox.  This will not happen.  The genbox program is only hard-coded to update the topology in the case of water.  Thus, after solvating, one must determine the number of solvent molecules added (using grep, for example) and update the [ molecules ] directive of the topology to reflect the changes made to the system.

    A series of about 150 different equilibrated liquids validated for use with gromacs, and for the OPLS/AA and GAFF force fields, can be found at http://virtualchemistry.org

    Making a non-aqueous solvent box

    Choose a box density and box size. The size does not have to be that of your eventual simulation box - a 1nm cube is probably fine.  Generate a single molecule of the solvent. Work out how much volume a single molecule would have in the box of your chosen density and size. Use editconf to place a box of that size around your single molecule. Then use editconf to move the molecule a little bit off center. Then use genconf -rot to replicate that box into a large one of the right size and density. Then equilibrate thoroughly to remove the residual ordering of the molecules, using NVT and periodic boundary conditions. Now you have a box you can pass to genbox -cs, which will replicate it to fit the size of the actual simulation box.

    Page last modified 20:05, 12 Jan 2014 by spoel