To verify that AMBER and NAMD give the same results

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** 原文地址** 通过计算范德华和静电相互作用来进行比较amber和namd的计算结果。

AMBER example point calculation (GB) input: 

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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: 

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# 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: 
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 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: 
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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