[gmx-users] Bad calculated Free Energy values

[Ilya Chorny]

How many lambda values are you using?

Ilya

  -----Original Message-----
  From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Alexandre Suman de Araujo
  Sent: Friday, April 02, 2004 3:26 AM
  To: gmx-users
  Subject: [gmx-users] Bad calculated Free Energy values


  Hi GMX-ers!!!

  I?m performing some simulations to obtain free energy of hydration of some
ions (Ca+2, Sr+2 and Ba+2) using oplsaa(tip3p for water) force field and the
results aren?t so good in my opinion. Look at the results below and the
experimental values (taken from book Burgess, Metal Ions in Solution):

  DGh (kJ/mol)

  Ion           Calculated          Experimental        Difference

  Ca+2         -1391                  -1591                        200
  Sr+2         -1248                  -1442                        194
  Ba+2         -1107                  -1317                        210


  Look that the difference between calc. and exp. values are something about
200 kJ/mol, then I think this can be something I?m not including in the
calculations that results in error with almost same values in three cases.

  The .mdp file that I?m using is this one:

  ;
  ;       Input file
  ;
  title               =  Calculo da energia livre de solvatacao do ion de Na
em H2O       ; a string
  cpp                 =  /lib/cpp                 ; c-preprocessor
  dt                  =  0.001                    ; time step (ps)
  integrator          =  md                       ; Tipo de simulacao a
fazer
  nsteps              =  800000                   ; number of steps
  ;Faca energia livre
  free_energy         =  yes                      ; calcule a energia livre
  init_lambda         =  0                        ; valor inicial de lambda
  delta_lambda        =  1.25e-6                  ; 1/n_passos
  nstcomm             =  1                        ; reset c.o.m. motion
  nstxout             =  100                      ; write coords
  nstvout             =  100                      ; write velocities
  nstlog              =  100                      ; print to logfile
  nstenergy           =  100                      ; print energies
  nstlist             =  10                       ; update pairlist
  ns_type             =  grid                     ; pairlist method
  pbc                 =  xyz                      ; Usar PBC em todas as
direcoes
  rlist               =  1.3                      ; cut-off for ns
  coulombtype         =  Cut-off                  ; Usa cut-off por causa do
calculo de e livre.
  rcoulomb            =  1.3                      ; cut-off for coulomb
  fourierspacing      =  0.12                     ; Parametro pra PME
  pme_order           =  4                        ; Parametro pra PME
  ewald_rtol          =  1e-5                     ; Parametro PME
  optimize_fft        =  yes                      ; Optimiza a FFT, claro..
hahah
  vdwtype             =  cut-off                  ; Tipo de VdW
  rvdw                =  1.3                      ; raio de calculo de Vdw
  tcoupl              =  berendsen                ; Temperature coupling
  ref_t               =  300                      ; Temperatura referencia
  tc-grps             =  System                   ; Quais grupos sera
afetados pelo tcoupl
  tau_t               =  0.01                     ; Tempo que sera
verificada a temperatura
  pcoupl              =  berendsen                ; pressure bath
  pcoupltype          =  isotropic                ; pressure geometry
  tau_p               =  1                        ; p-coupoling time
  compressibility     =  4.4e-5                   ; compressibilidade da
acetonitrila
  ref_p               =  1.0


  Somebody could help me telling me if I?m forgetting anything or making
something wrong?
  Or this difference is normal in free energy calculations????

  Thank?s very much and waiting answers.


--
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - Sao Carlos -
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