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 -- 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