FEP with slow-growth method

User discussions
1

GROMACS version: 2020.3

Dear all,

I am calculating free energy perturbation (FEP) for converting state A to state B and vice versa using the following for the free energy variables in the mdp file:

free-energy = yes
init-lambda = 0 (and 1 for B state)
delta-lambda = 1e-5 (and -1e-5 for B state)
sc-alpha = 0.3
sc-sigma = 0.25
sc-power = 1
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = yes
nstcalcenergy = 1
nstdhdl = 1

It seems that the equilibration and transition runs go well, but I have problems with analyzing the results.
My question is if it’s possible to use “gmx bar” to analyze such a system? And if not, what are the alternatives?

Thanks,
Mehrnoosh

2

Hi,

My question is if it’s possible to use “gmx bar” to analyze such a system?

No

And if not, what are the alternatives?

You can use gmx energy -odh to extract dh/dl

Best regards
Alessandra

3

Dear Alessandra,

Thank you so much for your reply.

Can you explain a bit more how I can use gmx energy? Now I have several xvg files as my output for different frames that I got from gmx mdrun -dhdl frame{i}.xvg; and there is no dH data in my edr files. Are my mdrun calculations wrong?

Thank you for your time.

Best regards,
Mehrnoosh