Steven Neumann wrote:
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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
--
========================================
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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