[gmx-users] Problem with energy minimization parameters

[Sainitin Donakonda]

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