[gmx-users] Question of free energy calculation

[qian wang]

Dear all,

I am using gromacs 4.5.4 to calculate the free energy change of a protein
from state A to state B.

The only part I want to perturb is the 1-4 interactions. So I changed the
original top from:

[ pairs ]
; i j type and weights
1527   1599 1   1.283754192E+00   4.120062062E-01

to
[ pairs ]
; i j type and weights
1527   1599 1   1.283754192E+00   4.120062062E-01   1.283754192E-05
4.120062062E-05

The free energy part in my mdp file is:

free_energy = yes
init_lambda = 0.0  ; should be in state A only
delta_lambda = 0.0
nstdhdl = 20

And it gives me a segmentation fault. If I change free_energy = no then it
is fine. So it is clear that I did something wrong in the free energy
calculation part. Could anyone help me? Thank you very much.

Sincerely,
Qian