[gmx-users] free energy calculations with flexable SPC

[Ilya Chorny]

Hi 

I ran two test simulations calculating the free energy of mutation of Ar
to an Ar atom with a smaller sigma in H2O. If I use flex water molecules
I get a ridiculous number approx 7500 KJ/mol but if I use rigid water I
get approx -4 KJ/mol which seems much more reasonable. Is there a reason
for this?

Thanks

Ilya

My mdp file:

cpp                 =  /lib/cpp
define              =  DFLEX_SPC  - with and without
integrator          =  md
dt                  = .001
nsteps              =  5000
nstenergy           =  20
nlist               =  1
coulombtype         =  Shift
vdwtype             =  Shift
rcoulomb_switch     =  1.0
rcoulomb            =  1.2
rvdw_switch         =  .8
rvdw                =  1.0
rslist              =  1.3
pbc                 =  xyz
tcoupl              =  no
pcoupl              = no
gen_vel             = yes
gen_temp            = 300
gen_seed            = -1
free_energy         = yes