GROMACS version: 5.1.4
GROMACS modification: No
Hi all,
I am writing you cause I am in trouble and not sure about the correctness of my results.
Briefly, I set up a free-energy perturbation with the slow-growth approach. Hence, lambda value slightly increase at each MD step.
I have 10 different MDs
Here the free-energy section of my fep.mdp file:
; Free energy control stuff
free_energy = yes
init_lambda = 0
delta_lambda = 0.00000004
sc-alpha = 0
sc-sigma = 0.3
Of course TypeB section in the topology is modified accordingly.
Calculations goes fine and at the end i get a file named ‘fep.xvg’ containing dH/dLambda along the frames. So far clear.
However, I have a doubt about the numerical integration step to obtain the free energy going from lambda=0 to lambda=1
I have tried gmx bar as follow:
gmx bar -f fep.xvg (w/wo -g fep.edr) getting the following error:
“Fatal error:
While trying to read the lambda value from the file path: last directory in the path ‘fep.xvg’ does not contain a number”
I suppose such an error arises because gmx bar expect a fixed lambda value while here I have used a slow-growth approach.
Do you have any ideas/experiences/suggestions on the best way to better extrapolate FES?
Thanks in advance for any kind contribution.
Regards
VG