[gmx-users] Error energy minimization on protein with implicit water

[lina]

On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar <aiswarya.pawar at gmail.com> wrote:
>
> Dear Gromacs users,
>
> I have a MD simulated protein and i take frame from this and remove water
> and add water implicit in the interface and want to do energy minimization
> but while doing the minimization i get errors. The steps followed are-
>
> pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
> grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr
>
> The minim.mdp file =
>
> ; Lines starting with ';' ARE COMMENTS
> ; Everything following ';' is also comment
>
> title        = Energy Minimization    ; Title of run
>
> ; The following line tell the program the standard locations where to find
> certain files
> cpp        = /lib/cpp    ; Preprocessor
>
> ; Define can be used to control processes
> define          = -DFLEXIBLE
>
> ; 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 < 1.0
emtol = 1.0
> kJ/mol
> nsteps        = 5000        ; Maximum number of (minimization) steps to
> perform
> nstenergy    = 1        ; Write energies to disk every nstenergy steps
> energygrps    = System    ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> ns_type        = simple      ; Method to determine neighbor list (simple,
> grid)
> coulombtype    = cut-off      ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.0        ; long range electrostatic cut-off
> rvdw        = 1.0        ; long range Van der Waals cut-off
> constraints    = none        ; Bond types to replace by constraints
> pbc        = no        ; Periodic Boundary Conditions (yes/no)
>
> I get a note as =
> System has non-zero total charge: -4.999996e+00
>
> then i tried using genion step as=
>
> genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log
>
> then again the grompp step and mdrun .
> but while doing mdrun i get an error as=
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
>
> but here i have given nsteps as 5000 so why does it stop.
> --
> Aiswarya  B Pawar
>
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
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