[gmx-users] Re: Problem with energy minimization parameters

[Sainitin Donakonda]

Hi Justin,

Thanks for suggestion...and pointing out that there is problem with
topology ...now i checked ligand file..there hydrogens were not added
correctly..so swissparam tool was not correct topology .. now i corrected
it ..it works perfectly ..

Thanks a lot

Sainitin


On Tue, Jul 16, 2013 at 5:05 PM, Sainitin Donakonda <saigro16 at gmail.com>wrote:

> Hi all,
>
> I have 3 protein-drug complexes (same protein and different drugs)  i
> performed 20 ns molecular dynamics simulation..using same parameters (i
> mean energy minimzation parameters) ..2 of them was successful for MD
> simulation..(im using Charmm 27 Force field)
>
> But 1 drug protein complex is failed in Energy minimization step itself..
> showing following error
>
> *Error : whole protein drug complex
> *
> *
> *
> *708 particles communicated to PME node 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.*
> *This usually means that your system is not well equilibrated
>
> *
> Then i looked up
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> In this i followed up suggestions which are mentioned in diagnosing
> unstable system as follows.
>
> First i did energy minimization for protein alone which worked perfectly
> with out any error.
>
> Second i did energy minimization for ligand alone (with out protein)..this
> showed again following error..
>
> Error 2 : Ligand only
>
> Fatal error:
> *184 particles communicated to PME node 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.*
>
> So there is problem with small molecule...not with the protein ..here i
> think i should tune parameters in .MDP file..which i m just not getting how
> to do..
>
> here is the EM.mdp file..
>
> ; LINES STARTING WITH ';' ARE COMMENTS
> title        = Minimization    ; Title of run
> define                  = -DFLEX_TI3P    ; defines to pass to the
> preprocessor
> constraints             = none
>
> ; 7.3.3 Run Control
> integrator              = steep         ; steepest descents energy
> minimization
> nsteps                  = 2000          ; maximum number of steps to
> integrate
> energygrps              = LIG        ; group(s) to write to energy file
>
> ; 7.3.5 Energy Minimization
> emtol                   = 1000          ; [kJ/mol/nm] minimization is
> converged when max force is < emtol
> emstep                  = 0.01          ; [nm] initial step-size
> dt                      = 0.01
>
>
> ; 7.3.9 Neighbor Searching
> nstlist                 = 1            ; [steps] freq to update neighbor
> list
> nstxout                 = 1
> ns_type                 = grid          ; method of updating neighbor list
> pbc                     = xyz           ; periodic boundary conditions in
> all directions
> rlist                   = 1.2           ; [nm] cut-off distance for the
> short-range neighbor list
> rlistlong               = 1.4           ; [nm] Cut-off distance from the
> long-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME           ; Particle-Mesh Ewald
> electrostatics
> rcoulomb                = 1.2           ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype                 = switch       ; twin-range cut-off with rlist
> where rvdw >= rlist
> rvdw                    = 1.2           ; [nm] distance for LJ cut-off
> rvdw_switch             = 0.2           ; Start switching th LJ potential
> DispCorr                = Ener          ; apply long range dispersion
> corrections for energy
>
> ; 7.3.13 Ewald
> fourierspacing          = 0.12          ; [nm] grid spacing for FFT grid
> when using PME
> fourier_nx              = 0
> fourier_ny              = 0
> fourier_nz              = 0
> pme_order               = 4             ; interpolation order for PME, 4 =
> cubic
> ewald_rtol              = 1e-5          ; relative strength of
> Ewald-shifted potential at rcoulomb
> optimize_fft            = yes
>
>
> Can any body please tell me how to optimize these parameters
>
> Thanks,
> Nitin
>