CCL: Salt bridges, H-bonds, aromatic stacking in MD?

 CCLers:
 I am looking at the interaction of a bound peptide and a target enzyme
 with EM and MD simulations. The peptide is docked into the active site,
 and lies, extended, across the protein, plugging a 'hole'
 on the surface of the protein.  I have three queries:
 ---------------
 Q1: Salt bridge...
 My major concern is that I have noticed that a salt-bridge between a
 surface Arg on the protein and a bound peptide Asp residue lengthens
 from ~4.0 ang. when docked to > 6.0 ang. during the MD portion of an
 EM/MD run.  It seems to fluctuate by about 1 ang., but over 100 ps
 doesn't shorten to ~4.0 ang. again.
 The system is in a large solvated sphere, and calculations are run on
 Discover 95 with CVFF using the default water model.
 As per advice from MSI, the cutoffs are set thus
 (i.e. double cutoffs, no switching function):
        cutoff=13.00
        cutdis=12.00
        swtdis=0
        cutof2=15.00
        cutds2=14.00
        swtds2=0
 Is this observation considered 'normal' given the conditions of the
 calculations, or should I be concerned?
 -------------
 Q2: Intermolecular hydrogen bonds...
 Similar to Q1, I also see certain intermolecular H-bonds lengthen
 to > 4.0 ang. (acceptor - donor) during MD simulations, and fluctuate
 about this longer distance (i.e. 3.5 - 4.5 ang).
 Again, is this considered 'normal' given the conditions of the
 calculation, or should I be concerned?
 -------------
 Q3: Aromatic stacking...
 Can anybody indicate how successful the CVFF forcefield is at simulating
 aromatic-aromatic stacking interactions?  I notice that phenyl rings in
 the active site pocket of the enzyme re-orient with respect to ligand,
 and appear to adopt 'favourable' edge-on, tilted-T, etc. orientations,
 depending on the ligand.
 How 'realistic' (within context) are these observations likely to be?
 -------------
 Can anybody offer any insights into these phenomena?
 Thanks in advance,
 Nick
 ____
 Nick Glover
 Department of Chemistry
 Simon Fraser University
 8888 University Drive
 Burnaby, BC
 V5A 1S6
 Canada
 Tel: (604) 291-4531
 Fax: (604) 291-3765
 email: nglover-: at :-sfu.ca