[gmx-users] .mdp file settings for thermodynamic integration

deepak bapat dubapat at gmail.com
Tue Apr 11 08:18:44 CEST 2017

Dear Gromacs users

I had a doubt regarding .mdp options for free energy using constrained

If i wish to change a bond length from l_A to l_B (say for example from 0.5
nm to 5 nm.  this bond will be used in the form of constraints type 2.
something similar to what is shown in manual of gromacs v 5.1.2 in
section *5.8.5
page no 151-152*) for doing thermodynamic integration instead of BAR.

I would be only varying this bond length and no other parameters such as
charge, mass.

would the following settings which i have shown in *case 1* and *case 2* in
mdp options yield same results?

*Case 1 mdp settings:*

init-lambda = 0.4 ; (i.e. for separation of (0.4*0.5+(1-0.4)*5=3.2 nm)
delta_lambda = 0
nstdhdl = 10
*case 2 mdp optoins:*

init-lambda-state = 4 ; column corresponding to 0.4 in bonded lambdas
;                            col0   col1   col2    col3    col4
bonded-lambdas =  0     0.1      0.2      0.3     0.4 ......... 1.0
delta_lambda = 0
; all other lambda such as mass lambda, coul lambda being set to 0 for all

Is case1 identical to case 2?


Deepak U. Bapat

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