Dear all, Thanks to everybody who replied to my question about making bonds between protein subunits - it is greatly appreciated ! I have another question: In order to improve the implementation of the calcium in my MD simulation, I would to make a few changes to the force-field (GROMOS-87), in particular the charges and van-der-Waals properties of the atoms in the vicinity of the Calcium. I have found descriptions in the literature on how these parameters are affected by calcium, but I am having problems including this information in my GROMACS setup. In particular, I would like to change the values in the ffgmxnb.itp file. Example: Take two atomtypes, O and OA. [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OA 15.99940 0.000 A 0.22617E-02 0.15062E-05 [ nonbond_params ] ; i j func c6 c12 O OA 1 0.22617E-02 0.13807E-05 [ pairtypes ] ; i j func cs6 cs12 O OA 1 0.22617E-02 0.74158E-06 The Question I have is this: How are the C6 and C12 values of the individual atomtypes related to the values found in the 'nonbond_params' and 'pairtypes'. In other words: once I have the C6 and C12 values of the atomtypes, how do I get to the values in the nonbond_params and pairtypes section ? What's the mathematical relationship between them ? It's obvious that some of the values are identical - is this because (in my example), the two atoms O and OA are sufficiently similar. Or is this a general property of these values ? Thank you in advance to anybody who replies, Chris ----------------------------------------- Christoph Meier Laboratory of Molecular Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3BW U.K. Phone +44 1865 275380 Email christoph.meier@hertford.ox.ac.uk -----------------------------------------