Difference between revisions of "NAMD Amber inputs"
From Rizzo_Lab
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| + | == 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: | AMBER gives the following results: | ||
NSTEP ENERGY RMS GMAX NAME NUMBER | NSTEP ENERGY RMS GMAX NAME NUMBER | ||
1 6.9509E+03 1.8660E+01 7.7702E+02 HD12 807 | 1 6.9509E+03 1.8660E+01 7.7702E+02 HD12 807 | ||
| − | + | ||
BOND = 216.2588 ANGLE = 724.0684 DIHED = 2516.9902 | BOND = 216.2588 ANGLE = 724.0684 DIHED = 2516.9902 | ||
VDWAALS = -1292.7545 EEL = -19141.1870 EGB = -3682.0180 | VDWAALS = -1292.7545 EEL = -19141.1870 EGB = -3682.0180 | ||
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ESURF = 14081.5300 | 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: | NAMD gives the following results: | ||
| − | ETITLE: TS BOND ANGLE DIHED IMPRP | + | ETITLE: TS BOND ANGLE DIHED IMPRP |
| − | + | ENERGY: 0 216.2589 724.0641 2516.9907 0.0000 | |
| − | 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 | Note that the NAMD VDW = AMBER VDWAALS + 1-4 VDW, and like-wise for ELECT | ||
Latest revision as of 11:43, 20 July 2009
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
