[gmx-users] error while energy minimization with the protein fixed

[Mark Abraham]

On 6/10/2011 11:54 PM, prakash verma wrote:
> Dear All,
>
> while energy minimization with the protein fixed i am getting 
> following error:
>
>
> *t = 0.011 ps: Water molecule starting at atom 21089 can not be settled.
> *

Rigid water models and EM are not a great combination. define = 
-DFLEXIBLE in the .mdp file is usually a good idea.
Position restraints are normally a better idea than frozen atoms for EM.

Mark

> *Check for bad contacts and/or reduce the timestep.*
> Even if i am reducing timesteps its not working.
> The minim.mdp file which i have used is:;
>
>
> ntegrator      = steep         ; Algorithm (steep = steepest descent 
> minimization)
> emtol           = 1000          ; Stop minimization when the maximum 
> force < 1000.0 kJ/mol/nm
> dt              = 0.01
> emstep          = 0.01          ; Energy step size
> nsteps          = 20000         ; Maximum number of (minimization) 
> steps to perform
>
> constraints     =  all-bonds    ; convert all bond to constraints
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist         = 5             ; Frequency to update the neighbor 
> list and long range forces
> ns_type         = grid          ; Method to determine neighbor list 
> (simple, grid)
> rlist           = 1             ; Cut-off for making neighbor list 
> (short range forces)
> coulombtype     = PME           ; Treatment of long range 
> electrostatic interactions
> rcoulomb        = 1             ; Short-range electrostatic cut-off
> rvdw            = 1             ; Short-range Van der Waals cut-off
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
> optimize_fft             = yes
> pme_order                = 4
> fourierspacing           = 0.15
> ; Non-equilibrium MD stuff
> freezegrps               = Protein Sol
> freezedim                = Y Y Y   N N N
>
>
> Regards,
> Prakash.
>
>

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