[gmx-users] vacuum simulations

[João Henriques]

Dear Tasneem,

Like on previous replies to your last email, people need to understand what
is the purpose of your simulation(s), otherwise it is difficult to help.
"Cooking" and "simulating" are two completely different things, there is no
recipe for the latter. One needs to understand what one wants to do in the
first place, and then what each parameter means and how it influences the
results. One should never fall into the temptation of using someone else's
.mdp files blindly. Many things have become *de facto* over the years, most
of the times for no other good reason besides the fact that some important
name in the field has been using it...

Best regards,
João

On Wed, Sep 2, 2015 at 12:06 PM, tasneem kausar <tasneemkausar12 at gmail.com>
wrote:

> Dear gromacs users
>
> I have performed the vacuum simulation of protein.
> The structure was minimized after generating the box using the following
> mdp parameters.
> ;
> ;    User spoel (236)
> ;    Wed Nov  3 17:12:44 1993
> ;    Input file
> ;
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  hbonds
> integrator          = steep
> nsteps              =  3000
> ;
> ;    Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
>
> nstcomm             =  1
> ns_type             =  simple
> rlist               =  0.0
> coulombtype         =  cut-off
> rcoulomb            =  0.0
> rvdw                =  0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl              =  no
> Pcoupl              =  no
> PBC                 =  no
> gen_vel             =  no
>
>
> then i have run the full md for 5ns.
> mdp parameter are as follows:
>
> ;
> ;    User spoel (236)
> ;    Wed Nov  3 17:12:44 1993
> ;    Input file
> ;
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> constraints         =  hbonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  2500000    ; total 5000 ps.
> nstcomm             =  1
> nstxout             =  500000
> nstvout             =  500000
> comm-mode           =  ANGULAR
> lincs_iter          =  2
> nstfout             =  0
> nstlog              =  500
> nstenergy           =  500
> nstxtcout           =  500
> xtc-precision       =  1000
> nstlist             =  10
> ns_type             =  simple
> rlist               =  0.0
> coulombtype         =  cut-off
> rcoulomb            =  0.0
> rvdw                =  0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  no
> tc-grps            =  Protein
> tau_t               =  0.1
> ref_t               =  300
> ; Energy monitoring
> energygrps          =  Protein
> ; Isotropic pressure coupling is now on
> Pcoupl              =  no
> Pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> PBC                 =  no
>
>
> Is this a right way to perform the MD in vacuum?
> Anyone if familiar with this procedure, please suggest.
>
>
> Thanks in Advance
> --
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