[gmx-users] Implicit solvent - Gromacs 4.5.4

[Mark Abraham]

On 29/02/2012 9:26 PM, Steven Neumann wrote:
>
>
> On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <mailto: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?
>

I have suggested such equilibration protocols in the past for implicit 
solvent - maybe 1ns is excessive. I've had simple peptide systems with 
no atomic clashes that have wanted such gentle treatment.

Mark
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