[gmx-users] problem during Energy minimization

Sat May 21 12:49:25 CEST 2011

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