[gmx-users] epsilon r

[jozef hritz]

I have probably naive question. Very often we simulate protein in big box
of explicit water molecules with epsilon r=1. It would be correct if we
have polarizability in force field, but we haven't. Are there some
correction from this point of view in charges of water molecule. If not
isn't it better to use higher value of epsilon r? The question is what
value, when for water it's 78 and for proteins around 4. Is it possible to
put different epsilon r into different regions (e.g. inside and outside of
protein)? 

Next thing is concerning with implicit solvent. In mailing list I red that
Erik had problems with effective calculation of protein surface so there
was problem with dynamics (how does it look now?). Is it possible to
implement implicit solvent for single point calculations?  

	Thank You very much
								Jozef