AMBER Archive (2000)

Subject: constrained MD

From: Minmin Wang (mwang_at_emory.edu)
Date: Wed Jul 12 2000 - 13:28:30 CDT

Dear Amber Users,

I am dealing with a large protein whose binding site is close to the
surface. I did a MD run in gas phase with distance dependent dielectric
constant and found sveral highly flexible residues at the binding site.
Then I did another MD simulation with solvent shell to constrain those
surface residues (with cut=9.0 and 18.0 ) and found those highly flexible
residues in my previous gas phase run were pretty much holding at their
original position. Instead residues in another region began to show large
movement during the simulation (10ps). Will this be the result of energy
migration( because of the constraint from the solvent) or would any of you
give me some suggestion how I can set up the system properly to monitor
the MD?

Thank you in advance,

Minmin

==============================================
Minmin Wang
Chemistry Department, Emory University
1515 Pierce Dr., Atlanta, GA 30322
Tel:404-7276631 Fax: 404-7276586
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