AMBER Archive (2002)

Subject: Polarizability, a general question

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Wed Sep 11 2002 - 03:56:32 CDT

Dear AMBERs,

I study proteins with X- ions in the active site. It is well known that
for big ions is not polarizability negligible (Br-, I-). I would like to
ask some questions about MD of proteins with polarizability.

1. How deep layer has one to use for study of X- ion in burried active
site? Has one to apply polarizability for whole system (ion, protein,
waters)? Can one use polarizability only with selected atom types (e.g. O*
etc)?

2. Why are partial charges scaled? Why to use different scaling for
protein and for waters? Does exist any general rules for charge scaling?

3. Which is the best water type for MD with polarizability (TIP....)?

4. How many times is MD with polarizability slower than normal MD?

Thank you in advance for your experiences, views, suggestions, literature
etc.

Michal Otyepka

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