[gmx-users] Implicit solvent - Gromacs 4.5.4

[Steven Neumann]

On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>> I run energy minimization of my protein with implicit solvent:
>>
>>    constraints = none
>>
>>    integrator = steep
>>
>>    dt = 0.001 ; ps
>>
>>    nsteps = 30000
>>
>>    vdwtype = cut-off
>>
>>    coulombtype = cut-off
>>
>>    pbc = no
>>
>>    nstlist = 0
>>
>>    ns_type = simple
>>
>>    rlist = 0 ; this means all-vs-all (no cut-off),
>>
>>    which gets expensive for bigger systems
>>
>>    rcoulomb = 0
>>
>>    rvdw = 0
>>
>>    comm-mode = angular
>>
>>    comm-grps = Protein
>>
>>    optimize_fft = yes
>>
>>    ;
>>
>>    ; Energy minimizing stuff
>>
>>    ;
>>
>>    emtol =
>>
>>    5.0
>>
>>    emstep = 0.01
>>
>>    ;
>>
>>    ; Implicit solvent
>>
>>    ;
>>
>>    implicit_solvent = GBSA
>>
>>    gb_algorithm = OBC
>>
>>    nstgbradii = 1
>>
>>    rgbradii = 0 ; [nm] Cut-off for the calculation of the
>>
>>    Born radii. Currently must be equal to rlist
>>
>>    gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent
>>
>>    ; gb_saltconc = 0 ; Salt concentration for implicit solvent
>>
>>    models, currently not used
>>
>>    sa_algorithm = Ace-approximation
>>
>>    sa_surface_tension = 2.25936
>>
>>  And I obtained:
>>
>> Steepest Descents:
>>
>> Tolerance (Fmax) = 1.00000e+03
>>
>> Number of steps = 30000
>>
>> Step Time Lambda
>>
>> 0 0.00000 0.00000
>>
>>
>>
>> Steepest Descents converged to Fmax < 1000 in 1 steps
>>
>> Potential Energy = inf
>>
>> Maximum force = 0.0000000e+00 on atom 0
>>
>> Norm of force = nan
>>
>>
>> Can you please explain?
>>
>>
> Not without more information.
>
> 1. What is in the system?     - protein without specified box
> 2. Which version of Gromacs is this?    - Gromacs 4.5.4
> 3. Are you using GPU or CPU architecture?   - I run it straight from the
> cluster on a specific node
> 4. Does an in vacuo minimization work (i.e., just turn off the GB parts)?
> - yes, it works


What shoould be the value for emtol in implicit solvent model with protein
with app. 150 residues?

Thank you,

Steven

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