[gmx-users] Implicit solvent problems

[liaoxyi]

Hi, dear all,

I’m doing the simulation involved in protein and some surface.

I encounter this problem when trying to use implicit solvent model 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.

  

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?

 

Is the minimization necessary for implicit solvent?

Thank you again for your reading.

 

Kiara


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