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

[David van der Spoel]

Mu Yuguang (Dr) wrote:
> Dear All,
> 
> How to output the vectors of pricipal axes calculated from the g_gyrate?
> 
>  
You'll have to edit the code, at line 253 in gmx_gyrate.c you will see 
the following:

#ifdef DEBUG
     pr_rvecs(stderr,0,"trans",trans,DIM);
#endif

If you change it to

     if (debug)
       pr_rvecs(debug,0,"trans",trans,DIM);

you can select printing of the matrix to the g_gyrate.log file by 
setting the -debug flag on the command line.

> 
> 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 <mailto:asaraujo at if.sc.usp.br>
> 
> UIN: 6194055
> 
> IFSC - USP - São Carlos - Brasil
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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