[gmx-users] Implicit solvent problems

Dallas Warren Dallas.Warren at monash.edu
Wed Oct 12 23:16:02 CEST 2011

Did you look at atom 2073?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of liaoxyi
Sent: Wednesday, 12 October 2011 3:59 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Implicit solvent problems

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.


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