[gmx-users] Re: gmx-users Digest, Vol 65, Issue 65

[Justin A. Lemkul]

Please delete any unrelated information from digests before replying.  It makes 
searching the archives much more efficient :)

I was referring to the actual parameters for your model and the basis you have 
for using them.  Are these something you're deriving?  Or some new parameter set 
you're trying to develop?

Did energy minimization converge to an acceptable value for the potential and 
maximum force?  Did your equilibration indicate a stable system (in terms of 
pressure, density, temperature, etc)?

-Justin

Nilesh Dhumal wrote:
> this is for Energy minimization
> title               =  EMI-BF4
> cpp                 = /usr/bin/cpp
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  50000
> nstlist             =  10
> coulombtype         = PME
> vdwtype             = cut-off
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.4
> fourierspacing      = 0.12
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
> pbc                 = xyz
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> 
> 
> this is for Equilibration
> 
> title               =  EMI-BF4
> cpp                 =  /usr/bin/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  200000      ; total 1.0 ps.
> nstcomm             =  1
> nstxout             =  10
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         = PME
> vdwtype             = cut-off
> rcoulomb            =  1.0
> rvdw                =  1.4
> 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
> Tcoupl = v-rescale
> tau_t = 0.1
> tc-grps  =system
> ref_t =   400
> ; Pressure coupling is  on
> Pcoupl              = parrinello-rahman
> pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  400.0
> 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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