[gmx-users] pr.mdp file

[Justin A. Lemkul]

Quoting s lal badshah <shahbiochemist at yahoo.com>:

> Dear Justin and Mark,
> My pr.mdp file is:
>
> title           = pr.mdp
> cpp             = /usr/bin/cpp
> define          = -DPOSRES
> constraints     = all-bonds
> integrator      = md
> dt              = 0.002
> nsteps          =100000
> nstcomm         = 1
> nstxout         = 250
> nstvout         = 1000
> nstlog          = 10
> nstenergy       = 10
> nstlist         = 10
> ns_type         = grid
> rlist           = 1.0
> coulombtype     = PME
> rcoulomb        = 1.0
> vdwtype         = cut-off
> rvdw            = 1.4
> fourierspacing  = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e5
> optimize_fft    = yes
> ;Berendsen temperature coupling is on
> Tcoupl          = berendsen
> tau_t           = 0.1      0.1  0.1
> tc-grps          = protein SOL NA+
> ref_t           = 298      298  298

Never couple solvent and ions separately.  This has been discussed several times
over the list.  Read here for advice:

http://wiki.gromacs.org/index.php/thermostats

-Justin

> ;Pressure coupling is on
> Pcoupl          = berendsen
> tau_p           = 0.5
> compressibility = 4.5e-5
> ref_p           = 1.0
> ;Generate velocities is on at 298 K
> gen_vel         = yes
> gen_temp        = 298
> gen_seed        = 173529
>
>
> As the warning is :
> Step 1  Warning: pressure scaling more than 1%, mu: -2.6855e+10 -2.6855e+10
> -2.6855e+10
>
> As the pressure is high so it shoud be how much?
> Regards,
> Lal badshah
>
>  Send instant messages to your online friends http://uk.messenger.yahoo.com



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Justin A. Lemkul
Graduate Research Assistant
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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