From: patrick wintrode (pat_wde2_at_yahoo.com)
Date: Thu Mar 31 2011 - 15:01:49 CDT
I've been testing out the new accelerated MD functionality in NAMD. I find that applying the boost just to the dihedrals works fine. However, if I use the dual boost mode, even quite small boost energies for the total-dihedral potential causes the simulation to become unstable and crash due to a constraint failure almost instantly (within ~15 steps).
My system is a 372 residue protein and the total system size protein+solvent is ~45,000 atoms.
The dihedral boost is E = 600 and alpha = 120. The smallest total-dihedral boost I've tried so far is E = 10 and alpha = 2.
Is my total-dihedral boost just too large? From reading the McCammon group's papers, it doesn't appear to be.
Any suggestions would be appreciated.
Patrick L. Wintrode
Dept. of Physiology & Biophysics
Case Western Reserve University
Cleveland, Ohio 44106
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