永远相信美好的事情终将发生

To verify that AMBER and NAMD give the same results

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