Difference between revisions of "NAMD Amber inputs"

Revision as of 11:31, 20 July 2009

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