# [gmx-users] Regarding Null free energy values in Free energy perturbation (bond force constant perturbation)

bipin singh bipinelmat at gmail.com
Mon Dec 22 16:05:42 CET 2014

```Hi all,

I am trying to perform a free energy perturbation calculation (using
Gromacs 4.6.3) to perturb the force constant of a bond (in vaccum), using
the B-state parameters in the topology as follows:

[ bonds ]
;  ai   aj  funct   c0         c1                    c0B       c1B
3    4    2   0.1090   1.2300e+07      0.1090 6.1500e+08

I have used 20 intermediate states between lambda=0 and 1. The MDP setting
(only some part shown) used for the calculation are as follows:

cutoff-scheme            = group
coulombtype              = cut-off
rcoulomb                 = 0.0
vdw-type                 = cut-off
rvdw                     = 0.0
pbc                      = no
nstlist                  = 0
ns-type                  = simple

free-energy              = yes
couple-moltype           = LIG
sc-power                 = 1
sc-alpha                 = 0.0
sc-r-power               = 6
sc-sigma                 = 0.3
sc-coul                  = no
couple-intramol         = yes
couple-lambda1          = vdw-q ; Do not change the non-bonded int. during
FEP
couple-lambda0          = vdw-q
init-lambda              = 0.0 (set accordingly for other intermediates)
delta-lambda             = 0
foreign-lambda           = 0.05 (set accordingly for other intermediates)
nstdhdl                  = 10
dhdl-print-energy        = no

But the final DG values with g_bar gives null values as shown below:

Final results in kJ/mol:

point  0.000 -  0.050,   DG  0.00 +/-  0.00
point  0.050 -  0.100,   DG  0.00 +/-  0.00
point  0.100 -  0.150,   DG  0.00 +/-  0.00
point  0.150 -  0.200,   DG  0.00 +/-  0.00
point  0.200 -  0.250,   DG  0.00 +/-  0.00
point  0.250 -  0.300,   DG  0.00 +/-  0.00
point  0.300 -  0.350,   DG  0.00 +/-  0.00
point  0.350 -  0.400,   DG  0.00 +/-  0.00
point  0.400 -  0.450,   DG  0.00 +/-  0.00
point  0.450 -  0.500,   DG  0.00 +/-  0.00
point  0.500 -  0.550,   DG  0.00 +/-  0.00
point  0.550 -  0.600,   DG  0.00 +/-  0.00
point  0.600 -  0.650,   DG  0.00 +/-  0.00
point  0.650 -  0.700,   DG  0.00 +/-  0.00
point  0.700 -  0.750,   DG  0.00 +/-  0.00
point  0.750 -  0.800,   DG  0.00 +/-  0.00
point  0.800 -  0.850,   DG  0.00 +/-  0.00
point  0.850 -  0.900,   DG  0.00 +/-  0.00
point  0.900 -  0.950,   DG  0.00 +/-  0.00
point  0.950 -  1.000,   DG  0.00 +/-  0.00

total  0.000 -  1.000,   DG  0.00 +/-  0.00

Please let me know, what could be the reason for this behavior.

*-------------------Thanks and Regards,Bipin Singh*
```