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

[Sainitin Donakonda]

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.

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