NAMD Amber inputs
From Rizzo_Lab
Point calculations to verify that AMBER and NAMD give the same results
AMBER example point calculation (GB) input:
Single point GB energy calc &cntrl ntf = 1, ntb = 0, ntc = 1, idecomp= 0, igb = 5, saltcon= 0.00, gbsa = 2, surften= 1.0, offset = 0.09, extdiel= 78.5, cut = 999.0, nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 1, ncyc = 0, &end
NAMD example point calculation input:
# initial config #coordinates GP41.WILD_t20.strip.solv.07md.pdb temperature 0 # output params outputname 07_to_11pr binaryoutput no # integrator params timestep 1.0 # force field params # Point Calc. for AMBER input files amber on parmfile active_erlotinib.com.gas.leap.parm ambercoor active_erlotinib.com.gas.leap.crd readexclusions yes # exclusions are taken from parmfile exclude scaled1-4 1-4scaling 0.833333 # =1/1.2, default is 1.0 scnb 2.0 # Defalt switching off cutoff 999.0 pairInteraction off ## Compute energies and forces, but don't try to move the atoms. run 0 ##coorfile close
AMBER gives the following results:
NSTEP ENERGY RMS GMAX NAME NUMBER 1 6.9509E+03 1.8660E+01 7.7702E+02 HD12 807 BOND = 216.2588 ANGLE = 724.0684 DIHED = 2516.9902 VDWAALS = -1292.7545 EEL = -19141.1870 EGB = -3682.0180 1-4 VDW = 1317.8423 1-4 EEL = 12210.1621 RESTRAINT = 0.0000 ESURF = 14081.5300
Note the following: VDWAALS + 1-4 VDW = -1292.7545 + 1317.8423 = 25.0878
and EEL + 1-4 EEL = -19141.1870 + 12210.1621 = -6931.0249
NAMD gives the following results:
ETITLE: TS BOND ANGLE DIHED IMPRP ENERGY: 0 216.2589 724.0641 2516.9907 0.0000
ELECT VDW BOUNDARY MISC KINETIC -6931.2673 25.0872 0.0000 0.0000 0.0000
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG -3448.8662 0.0000 -3385.0133 -3385.0133 0.0000
Note that the NAMD VDW = AMBER VDWAALS + 1-4 VDW, and like-wise for ELECT