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
--
========================================
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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