The first example illustrates the use of TCL scripting for running
an alchemical transformation with the FEP feature of NAMD. In this
calculation, is changed continuously from 0 to 1
by increments of
= 0.1.
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The user should be reminded that by setting run 10000, 10,000 MD steps will be performed, which includes the preliminary fepEquilSteps equilibration steps. This means that here, the ensemble average of equation (30) will be computed over 5,000 MD steps.
Alternatively, -states may be declared
explicitly, avoiding the use of TCL scripting:
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This option is generally preferred to set up windows of diminishing
widths as
0 or 1 -- a way to circumvent
end-point singularities caused by appearing atoms that may
clash with their surroundings.
The following second input is proposed for the measuring via TI the free energy of a particle insertion.
thermInt On # Enable thermodynamic integration tiFile ion.alch.pdb # PDB file with perturbation flags tiCol B # Perturbation flags in Beta column tiOutfile ion.ti.out tiOutFreq 5 tiEquilSteps 5000 tiVdWShiftCoeff 1 # Enable soft-core vdW potential tiElecLambdaStart 0.1 # Introduce electrostatics for lambda > 0.1 tiLambda 0 run 10000 tiLambda 0.00001 run 10000 tiLambda 0.0001 run 10000 tiLambda 0.001 run 10000 tiLambda 0.01 run 10000 set Lambda 0.1 while {$Lambda <= 0.9} { tiLambda $Lambda run 10000 set Lambda [expr $Lambda + 0.1] } tiLambda 0.99 run 10000 tiLambda 0.999 run 10000 tiLambda 0.9999 run 10000 tiLambda 0.99999 run 10000 tiLambda 1 run 10000
Robust
sampling of the free energy of particle insertion is enabled by the use of
soft-core van der Waals scaling with the VdWShiftCoeff parameter,
delayed introduction of electrostatics with a non-zero tiElecLambdaStart value, and very gradual scaling of towards its
end points.