[gmx-users] Slow-growth method question

Fabian Casteblanco fabian.casteblanco at gmail.com
Tue May 8 21:24:51 CEST 2012

Hello community,

I recently ran several simulations using the g_bar method on several
molecule decouplings and I even applied it to some functional group
mutations and it seems to work out quite well so far.  The only thing
is that it requires several simulations to run.  I'm attempting to
replicate this group mutation using the original slow-growth method
that others have done in the past just to see how well it compares to
the g_bar method.  I can't seem to find any sort of instructions on
running this method on Gromacs.    I have the parameters from g_bar
below but I'm trying to figure out how to alternate them below for the
slow growth method.  Is it simply the delta_lambda parameter that
needs to be changed?  Would I have to divide the timesteps by
delta_lambda to make sure it goes up to Lambda=1?  How do you
calculate the end result?    Thank you.

; Free energy control stuff
free_energy             = yes		
;*** - Indicates we are doing a free energy calculation, and that
interpolation between the A and B states of the chosen molecule
(defined below) will occur.

init_lambda             = 0.0		
;*** - Value of λ

delta_lambda            = 0		
;*** - The value of λ can be incremented by some amount per timestep
(i.e., δλ/δt) in a technique called "slow growth." This method can
have significant errors associated with it, and thus we will make no
time-dependent changes to our λ values.

foreign_lambda          = 0.05		
;*** - Additional values of λ for which ΔH will be written to dhdl.xvg
(with frequency nstdhdl). The configurations generated in the
trajectory at λ = init_lambda will have ΔH calculated for these same
configurations at all values of λ = foreign_lambda.

sc-alpha                = 0.5		
;*** - the soft-core parameter, a value of 0 results in linear
interpolation of the LJ and Coulomb interactions

sc-power                = 1.0		
;*** - the power for lambda in the soft-core function, only the values
1 and 2 are supported

sc-sigma                = 0.3 		
;*** - the soft-core sigma for particles which have a C6 or C12
parameter equal to zero or a sigma smaller than sc_sigma

;couple-moltype          = SIM  	
;*** - name of moleculetype to decouple

;couple-lambda0          = vdw		
;*** - all interactions are on at lambda=0
;couple-lambda1          = none     	
;*** - only vdw interactions are on at lambda=1
couple-intramol         = no		
;*** - Do not decouple intramolecular interactions. That is, the λ
factor is applied to only solute-solvent nonbonded interactions and
not solute-solute nonbonded interactions.

nstdhdl                 = 10		
;*** - The frequency with which ∂H/∂λ and ΔH are written to dhdl.xvg.
A value of 100 would probably suffice, since the resulting values will
be highly correlated and the files will get very large. You may wish
to increase this value to 100 for your own work.

Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering

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