[gmx-users] Gromacs free energy calculation using equilibrated system in Amber?
spoel at xray.bmc.uu.se
Sun Nov 9 23:55:01 CET 2003
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?
> 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 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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