[gmx-users] Implicit solvent - Gromacs 4.5.4

[Steven Neumann]

On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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
>>
>
> Doesn't answer the question, but I'll assume CPU since EM doesn't work on
> GPU's.  Just checking.
>
>
>    4. Does an in vacuo minimization work (i.e., just turn off the GB
>>    parts)?  - yes, it works
>>
>>
> And what is the output?
>
> In any case, I can't reproduce any problem doing EM with implicit solvent
> in 4.5.4 - my test systems work quite well.  It may just be that the system
> cannot be minimized because of some clash that is unfavorable in an
> implicit solvent environment (thus causing an immediate halt, though that
> would be odd) but can be resolved in vacuo.  Try using the structure
> produced by in vacuo minimization as input into the implicit solvent EM to
> see if this may be the case.
>
>
>
>> What shoould be the value for emtol in implicit solvent model with
>> protein with app. 150 residues?
>>
>>
> One that is sufficient for the inherent forces in the system and for your
> application ;)  I don't think there are any hard and fast rules here for
> standard MD, and the target is not dictated by the size of the protein.
>
>
> -Justin
>


Thank you Justin.

Mark, would you suggest equilibration e.g. for 1ns with no restraints and
no constraints in implicic solvent with timestep =0.0005 and then run MD
with implicit employing LINCS?

Steven

>
> --
> ==============================**==========
>
> 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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