[gmx-users] Steepest Descents converged to machine precision
sharmanitu35 at gmail.com
Mon Apr 27 10:15:09 CEST 2009
I explain you what I want to ask . I give you a detail of my processing -
* step for packing lipid around protein-
1. concatanation of protein and lipid bilayer in proper orientation- I did.
2.Inflate the bilayer by using inflategro script with scaling factor 4 and
cutoff 14- I did .
there is 8 lipid removed in this process and a/c to that I have update my
topology file .
3. Energy minimisation by applying strong position restrain on protein the
problem occur here is-
Step= 344, Dmax= 1.8e-05 nm, Epot= 4.29315e+06 Fmax= 1.02525e+05, atom=
Step= 349, Dmax= 1.4e-06 nm, Epot= 4.29315e+06 Fmax= 9.86524e+04, atom=
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 350 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.2931510e+06
Maximum force = 1.0252509e+05 on atom 4615
Norm of force = 1.3668822e+03
my em.mdp file-
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 10000
; Energy minimizing stuff
emtol = 1000
emstep = 0.001
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
comm-mode = Linear
pbc = XYZ
my topology file is like this-
; Include forcefield parameters
; Include DMPC chain topology
[ system ]
Protein in DMPC bilayer
[ molecules ]
; Compound #mols
1. probable reason of steepest descent converged to macine precision but
did not reach the requested Fmax < 1000.
2.The even after applying strong position restrain on protein the protein
structure being disturbed.
If u can make help for me . I will appreciate you.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users