Non-Water Solvation

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    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.

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