[gmx-users] Issue in Energy minimization protein-ligand complex

[Justin Lemkul]

On 7/4/13 3:00 PM, Sainitin Donakonda wrote:
> Hi all,
>
> I have set of 5 different drugs which are complexed with same protein
> (homology model). So i wanted to run MD simulation using gromacs. I
> followed one procedure as follows
>
> 1) I took homology model and minimized it
> 2) Then followed general procedure of simulation in gromacs.
>
> 4 drugs with same protein simulation was successful. Unfortunately 1 drug
> among these 5 drugs  showing error at energy minimization step although i
> used same em.mdp file which is used in other four simulations..
>
>
> *Error :*
> *
> *
> *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*
> *
> *
> This means system blowing up at energy minimization step itself ..just I
> dont know whats the problem..
>
> Can anybody tell me how to solve this issue..major problem here is same
> energy minimization step using .mdp file as mentioned above .dont know why
> this is failing for this particular protein-drug complex.
>

How did you prepare the initial configurations?  How did you create the ligand 
topology?  One or the other is your problem.

-Justin

> em.mdp which i used in in all 5 simulations as follows
>
> ; 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              = Protein 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                      = 0.002
>
>
> ; 7.3.9 Neighbor Searching
> nstlist                 = 5            ; [steps] freq to update neighbor
> list
> 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
>
>
> Thanks,
> sainitin
>
>
>
>
> Thanks,
> Sainitin
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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