[gmx-users] mdp file to calculate local pressure

Justin A. Lemkul jalemkul at vt.edu
Thu May 21 14:07:10 CEST 2009



anirban polley wrote:
> Dear Sir,
>              I want to calculate local pressure of the membrane 
> (pressure variation with z -axis). I am using gromacs-localp packages. 
> As I see that all types of errors coming from saying specifically the 
> option of WALL in .mdp file.
> Actually I did not understand clearly what to do in the following options.

The simple answer to me is - why are you using walls?  The gromacs-localp 
package is based on version 3.0.2, and IIRC walls were introduced much later in 
development, probably version 4.0.  At least, there is no mention of walls in 
any documentation prior to the 4.0 manual.

-Justin

> WALLS
> ; Number of walls, type, atom types, densities and box-z scale factor 
> for Ewald
> nwall                    = 2
> wall_type                = 9-3
> wall_r_linpot            = -1
> wall_atomtype            =
> wall_density             =
> wall_ewald_zfac          = 3
> 
> Could you please write clearly what to write on above options ??
> 
> I am writing here the mdp file what I am using in gromacs-localp package 
> to calculate local pressure.
> integrator           =  sd              ; stochastic dynamics -> Langevin!
> ld_seed              =  -1              ; random seed for sd
> dt                   =  0.002           ; ps !
> nsteps               =  50000           ; total 500/5=100 ps
> nstcomm              =  1               ; freq. for cm-motion removal
> tinit                =  0               ; starting time (ps)
> 
> constraints          =  all-bonds       ; constraint for all bond lengths
> constraint_algorithm =  lincs           ; default
> lincs_order          =  4               ; default
> 
> nstxout              =  1000            ; T(x_out) 10 ps
> nstvout              =  1000            ; T(v_out) 10 ps
> nstfout              =  0               ; T(f_out)
> nstlog               =  250             ; energies to log (0.5 ps)
> nstenergy            =  250             ; energies to energy file
> 
> ns_type              =  grid            ; nl type
> nstlist              =  10              ; Freq. to update neighbour list
> rlist                =  1.0             ; nm (cutoff for short-range nl)
>  
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc                      = xy
> 
> coulombtype          =  PME             ;Reaction-Field  ; Coulomb 
> interactions
> rcoulomb             =  1.0             ;2.0             ; nm (Coulomb 
> cut-off!!)
> epsilon_r            =  80.0            ; dielectric constant for 
> reaction field
> vdwtype              =  Cut-off         ; Wan der Waals interactions
> rvdw                 =  1.0             ; nm (LJ cut-off)
> optimize_fft         =  yes
> 
> ; Temperature coupling
> Tcoupl               =  no              ; no effect when integrator = sd
> tc-grps              =  POPC   SM   CHOL   SOL
> tau_t                =  0.1   0.1   0.1   0.1
> ref_t                =  296   296   296   296
> 
> ; Pressure coupling
> ;Pcoupl = no
> Pcoupl               =  berendsen
> Pcoupltype           =  semiisotropic
> tau_p                =  1.0    1.0       ; ps
> compressibility      =  4.5e-5 4.5e-5    ; 1/bar (water: 1 atm, 300 K)
> ref_p                =  1.0    1.0       ; bar
> 
> ; Generate velocites in the beginning
> gen_vel              =  yes
> gen_temp             =  296.0
> gen_seed             =  173529
> 
> ;WALLS
> ; Number of walls, type, atom types, densities and box-z scale factor 
> for Ewald
> nwall                    = 2
> wall_type                = 9-3
> wall_r_linpot            = -1
> wall_atomtype            =
> wall_density             =
> wall_ewald_zfac          = 3
> 
> Thanks a lot in advance.
> Regards,
> Anirban
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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