[gmx-users] problem during energy minimization before MD

[Itamar Kass (Med)]

Hi Parul,

First, what you get is not an error, it just says that your system can not
be minimised. Still, the high energy out of the EM might indicate a problem
in your system. Try to find and overlap between the protein and the
membrane, maybe you have a traped lipid molecule somewhere in your system.

All the best,
Itamar.

On 21 May 2011 20:47, Parul tew <parultew at gmail.com> 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_1.mdp –c system_inflated.gro 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.
>
>
>
> 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
>
>
>
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-- 

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================
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