[gmx-users] mdp file to calculate local pressure

[Justin A. Lemkul]

anirban polley wrote:
> Dear Justin,
>      I am using gromacs-localp of version 4.0.2. for the calculation of 
> local pressure. But I could not understand what I should put in the mdp 
> file. Because when I tried by the following below mdp file, it does not 
> even create tpr file. I have tried by different options as for example 
> by using Wall but failed to get local pressure profile. I thought that I 
> have write some thing so that it can be ok for giving local pressure. 
> Could you please correct my mdp file and write what extra term I should 
> write in my mdp file to get local pressure.
> Thank you very much for your kind help.

Where did you get gromacs-localp version 4.0.2?  The software by that name in 
the Users Contributions is much older.  If you have made modifications to the 
code yourself, you may have broken something.

As I understand it, the .mdp file is probably going to be the same as any other 
run, you'll just get additional output for local pressure.  That information is 
likely in whatever README or help files that come with the localp code.

Also, if grompp is failing to produce your .tpr, it is better to post the error 
message you got instead of saying "it does not even create tpr file."  For 
diagnostic purposes, a real error message is infinitely more useful.

-Justin

> Anirban
> 
>     title                =  lipid bilayer in water
> cpp                  =  /lib/cpp
> 
> integrator           =  sd              ; stochastic dynamics -> Langevin!
> ld_seed              =  -1              ; random seed for sd
> dt                   =  0.002           ; ps !
> nsteps               =  250000          ; total 500 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              =  5000            ; T(x_out) 10 ps
> nstvout              =  5000            ; 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)
> 
> coulombtype          =  Reaction-Field  ; Coulomb interactions
> rcoulomb             =  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
> 
> 
> ------------------------------------------------------------------------
> 
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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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