[gmx-users] Parameters for small molecule

Andrew Horsfield horsfield at fecit.co.uk
Mon Jan 14 12:39:24 CET 2002


I want to perform a simulation using both a small molecule and a large
protein. I would like to use accurate charges (from an electronic
structure calculation) for the small molecule. If I do not modify the
gromacs parameters I get a badly wrong geometry for the small molecule
when I relax it. So I must refit the bonding parameters, and use these
special values in the topology file. Is there a simple way to do this for
a small molecule? I could see 

It seems to me that using the following data from an electronic structure
program there ought to be an easy way to do this:

1) Relaxed coordinates
2) Atomc charges
3) Hessian matrix



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