[gmx-users] Gromacs free energy calculation using equilibrated system in Amber?

[Yuhua Song]

Hi, Gromacs developer and user:

Can I use the equilibrated system from Amber to calculate the free energy from Gromacs?

I see in the gromacs website: contribution part, there is a program to transform Amber format to
Gromacs format. 

I am wondering if I use this program, could I directly use the system well equilibrated in Amber
to calculate free energy perturbation using Gromacs?

The reason that I use Amber to equilibrate the system is when I use Gromcas to equilibrate
the system, the ion in the binding site always escape away from the binding site.
It is not realistic in the experimental. I also want to know how I can overcame the 
the phenomenon that ion escaping from binding site? The following is my *.mdp file.

Could you please help me out?

Thanks, 

Yuhua


The following is my *.mdp file.
;
;   User spoel (236)
;   Wed Nov  3 17:12:44 1993
;   Input file
;
title               =  production-Npt-300K
cpp                 =  /lib/cpp
constraints         =  hbonds
constraint_algorithm     = shake
shake-tol                = 1e-05
unconstrained_start      = no
integrator          =  sd
dt                  =  0.002    ; ps !
nsteps              =  1000000  ; total 2ns.
nstcomm             =  1
nstxout             =  1000
nstvout             =  50000
nstfout             =  0
nstlog              =  1000
nstenergy           =  1000
nstlist             =  20
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps         =  Protein HOH SOL NA CL
tau_t               =  0.1 0.1 0.1 0.1 0.1
ref_t               =  300 300 300 300 300
; Energy monitoring
energygrps      =  System
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites 0ff on at 300K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529