Difference between revisions of "NAMD Amber inputs"
From Rizzo_Lab
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ESURF = 14081.5300 | ESURF = 14081.5300 | ||
| − | + | Note the following: VDWAALS + 1-4 VDW = -1292.7545 + 1317.8423 = 25.0878 | |
| − | + | EEL + 1-4 EEL = -19141.1870 + 12210.1621 = -6931.0249 | |
| − | |||
NAMD gives the following results: | NAMD gives the following results: | ||
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TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG | TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG | ||
-3448.8662 0.0000 -3385.0133 -3385.0133 0.0000 | -3448.8662 0.0000 -3385.0133 -3385.0133 0.0000 | ||
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| − | |||
Note that the NAMD VDW = AMBER VDWAALS + 1-4 VDW, and like-wise for ELECT | Note that the NAMD VDW = AMBER VDWAALS + 1-4 VDW, and like-wise for ELECT | ||
Revision as of 11:27, 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 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
