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

[David]

On Sun, 2003-11-09 at 23:25, Yuhua Song wrote:
> Hi, Gromacs developer and user:
> 
> Can I use the equilibrated system from Amber to calculate the free energy from Gromacs?
> 
you want to sue the same forcefield for equilibration and free energy.

> I see in the gromacs website: contribution part, there is a program to transform Amber format to
> Gromacs format. 
> 
amber ascii can be read without conversion

> 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 be anything, most likely force field. Try OPLS forcefield


> 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
> 
> 
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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