On 12/10/2011 3:59 PM, liaoxyi wrote:
Hi, dear all,
I'm doing the simulation involved in protein and some surface.
I encounter this problem when trying to use implicit solventmodel with
GMX4.5.3.
First, minimize. When doing this I got the result as below:
Step=0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06, atom= 2073
Step=1, Dmax= 1.0e-02 nm, Epot= -1.99260e+06 Fmax= 1.05712e+06, atom= 2073
Step=2, Dmax= 1.2e-02 nm, Epot= -2.09734e+06 Fmax= 1.79058e+05, atom= 2073
Step=4, Dmax= 7.2e-03 nm, Epot= -2.17474e+06 Fmax= 7.22113e+04, atom= 2073
Step=6, Dmax= 4.3e-03 nm, Epot= -2.17724e+06 Fmax= 4.33926e+04, atom= 2073
Step=8, Dmax= 2.6e-03 nm, Epot= -2.18069e+06 Fmax= 3.24778e+04, atom= 2073
Step=10, Dmax= 1.6e-03 nm, Epot= -2.18404e+06 Fmax= 2.76114e+04, atom=
2073
Step=13, Dmax= 4.7e-04 nm, Epot= -2.18500e+06 Fmax= 2.63803e+04, atom=
2073
Step=17, Dmax= 7.0e-05 nm, Epot= -2.18514e+06 Fmax= 2.62045e+04, atom=
2073
Step=19, Dmax= 4.2e-05 nm, Epot= -2.18522e+06 Fmax= 2.61000e+04, atom=
2073
Step=22, Dmax= 1.3e-05 nm, Epot= -2.18524e+06 Fmax= 2.60689e+04, atom=
2073
Step=23, Dmax= 1.5e-05 nm, Epot= -2.18527e+06 Fmax= 2.60315e+04, atom=
2073
Step=27, Dmax= 2.3e-06 nm, Epot= -2.18527e+06 Fmax= 2.60258e+04, atom=
2073
Step=29, Dmax= 1.4e-06 nm, Epot= -2.18488e+06 Fmax= 2.60222e+04, atom=
2073
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 30 steps,
but did not reach the requested Fmax < 1000.
Potential Energy= -2.1852700e+06
Maximum force=2.6025840e+04 on atom 2073
Norm of force=2.2667976e+03
---------------------------------------
From above, the force is extremely large. And I don't know why.
Nobody can until you have a look at the structure before, during (after
using nstxout=1) and after the EM, and apply your chemical knowledge.
the minim.mdp is as below:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent minimization)
emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep= 0.01; Energy step size
nsteps= 50000; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range forces
ns_type= grid; Method to determine neighbor list (simple, grid)
rlist= 1.0; Cut-off for making neighbor list (short range forces)
coulombtype= Cut-off; for Implicit solvent long-range electrostatics
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)
; implicit_solvent
implicit_solvent= GBSA
gb_algorithm= OBC
nstgbradii= 1
rgbradii= 1.0
gb_epsilon_solvent= 78.3
gb_obc_alpha= 1; OBC(II)
gb_obc_beta= 0.8 ; OBC(II)
gb_obc_gamma= 4.85 ; OBC(II)
gb_dielectric_offset= 0.09
-----------------
Is there any item that's not proper or needed to add?
Seems fine.
Is the minimization necessary for implicit solvent?
Always wise.
Mark
Thank you again for your reading.
Kiara
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