[gmx-users] Implicit solvent problems

[Mark Abraham]

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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