[gmx-users] Implicit solvent - Gromacs 4.5.4

[Justin A. Lemkul]

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?
2. Which version of Gromacs is this?
3. Are you using GPU or CPU architecture?
4. Does an in vacuo minimization work (i.e., just turn off the GB parts)?

-Justin

-- 
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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

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