[gmx-users] how to output the vectors of pricipal axes from the g_gyrate

[Mu Yuguang (Dr)]

Dear All,

How to output the vectors of pricipal axes calculated from the g_gyrate?

 

Dr. Yuguang Mu

Division of Structural and Computational Biology

School of Biological Sciences

Nanyang Technological University

60 Nanyang Drive 

Singapore 637551

Tel: 63162885

Fax: 67913856

 

________________________________

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 7:26 PM
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 - São Carlos - Brasil
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