[gmx-users] problem during Energy minimization

[Justin A. Lemkul]

Parul tew wrote:
> Dear GMX users,
> 
>  I am facing problem while doing energy minimization before the 
> molecular dynamic simulation step of a system consisting of protein, 
> membrane, water and 14 ions.
> 
> The minim.mdp file is as follows
> 
> -------------------------------------------------------------------------------------------------------------
> 
> ; 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                  = 1.2                    ; Cut-off for making 
> neighbor list (short range forces)
> 
> coulombtype   = PME             ; Treatment of long range electrostatic 
> interactions
> 
> rcoulomb         = 1.2                ; Short-range electrostatic cut-off
> 
> rvdw                = 1.2                ; Short-range Van der Waals cut-off
> 
> pbc                  = xyz               ; Periodic Boundary Conditions 
> 
> *---------------------------------------------------------------------------------------------------------*
> 
> when I run this using the command
> 
> * *
> 
> *grompp –f minim.mdp –c system_sol_ions.gro -p topol.top –o em.tpr *
> 
>  
> 
>  then I invoked mdrun which gave following error
> 
> --------------------------------------------------------------------------------------------------------
> 
> Reading file topol.tpr, VERSION 4.0.7 (single precision)
> 
> Loaded with Money
> 
>  
> 
> Steepest Descents:
> 
>    Tolerance (Fmax)   =  1.00000e+03
> 
>    Number of steps    =        50000
> 
> Step=   14, Dmax= 1.2e-06 nm, Epot=  3.03531e+22 Fmax=         inf, 
> atom= 1417
> 
> 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.
> 
> You might need to increase your constraint accuracy, or turn
> 
> off constraints alltogether (set constraints = none in mdp file)
> 
>  
> 
> writing lowest energy coordinates.
> 
>  
> 
> Steepest Descents converged to machine precision in 15 steps,
> 
> but did not reach the requested Fmax < 1000.
> 
> Potential Energy  =  3.0353124e+22
> 
> Maximum force     =            inf on atom 1417
> 
> Norm of force     =            inf
> 
> -----------------------------------------------------------------
> 
> After this I changed the
> 
> emstep      = 0.1      ; Energy step size
> 
> nsteps          = 5000  ; Maximum number of (minimization) steps to perform
> 
> constraints     = none
> 
> After these changes the no of steps increased to 18 but still the system 
> did not converge and potential energy is very high
> 
> ----------------------------------------------------------------------------------------------------------
> 
>  
> 
> Reading file em.tpr, VERSION 4.0.7 (single precision)
> 
> Loaded with Money
> 
>  
> 
> Steepest Descents:
> 
>    Tolerance (Fmax)   =  1.00000e+03
> 
>    Number of steps    =         5000
> 
> Step=   17, Dmax= 1.5e-06 nm, Epot=  3.03531e+22 Fmax=         inf, 
> atom= 1417
> 
> 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.
> 
> You might need to increase your constraint accuracy, or turn
> 
> off constraints alltogether (set constraints = none in mdp file)
> 
>  
> 
> writing lowest energy coordinates.
> 
>  
> 
> Steepest Descents converged to machine precision in 18 steps,
> 
> but did not reach the requested Fmax < 1000.
> 
> Potential Energy  =  3.0353124e+22
> 
> Maximum force     =            inf on atom 1417
> 
> Norm of force     =            inf
> 
> ----------------------------------------------------------------------------------------------------------------
> 
> What changes can I do in my minim.mdp file to converge my system and get 
> a negative value of Epot.
> 

No amount of changes to the .mdp file will solve this.  If you have infinite 
forces, that indicates atomic overlap between some elements of the system that 
cannot be resolved.  The environment around atom 1417 is problematic.  Look at 
it in a visualization program and diagnose why it's happening.  Then generate a 
more stable configuration and try again.

-Justin

>  
> 
> The topol.top file looks
> 
> --------------------------------------------------------------------------------------------------
> 
> [ system ]
> 
> ; Name
> 
> protein
> 
> 128-Lipid DPPC Bilayer
> 
>  
> 
> [ molecules ]
> 
> ; Compound        #mols
> 
> Protein_A           1
> 
> DPPC                121
> 
>  
> 
> SOL             11107
> 
> CL-                              14
> 
> -----------------------------------------------------------------------------------------------------
> 
> Thanks,
> 
> Parul
> 
>  
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================