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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
