[gmx-users] Question of free energy calculation
qian wang
qq.wang630 at gmail.com
Tue Oct 20 23:40:58 CEST 2015
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
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