Hi Justin, Thanks for reply.
using pdbgmx i generated charmm27 force field for protein I prepared ligand topologies using swissparam online tool for all 5 ligands. But it worked for 4 and 5th one is creating problem at energy minimization step. Thanks -sainitin On Thu, Jul 4, 2013 at 9:02 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
