Accelerated Molecular Dynamics logs

From: Johny Telecaster (
Date: Sat Mar 08 2014 - 09:37:05 CST

Dear Namd Users!

I have one question about aMD logs

in log file of my simulation I've found

ACCELERATED MD: STEP 4195000 dV 40.4564 dVAVG 34.7729 BOND 1403.62 ANGLE
3937.04 DIHED 2561.44 IMPRP 260.601 ELECT -22616.8 VDW -4872.7 POTENTIAL

I wounder to know more about

dV 40.4564 dVAVG 34.7729

does this value corresponds to the summed additional boost potential added
to the overall system in kcal/mol ? (I'm using amd in dihedral boost only
regime). What difference between dV and dVAVG? What values for both terms
should be fine for system consisted of typical water soluble protein (400
residues) taking into accouint that I've used Jeff's impirical equation
for alpha and boost values ?

Thanks for help,


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