This usually means that your system is not well equilibrated.
Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 15, 2014 at 6:13 AM, Padmani Sandhu <padmanisandh...@gmail.com> wrote: > Hello, > > > I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded > in POPC lipid membrane. After energy minimizing of complex, I am facing > problem with NVT equilibration step. mdrun crashed with following error: > > > "12 particles communicated to PME node 4 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." > > > > > These are the parameters used in nvt.mdp file: > > title = NVT equilibration > > define = -DPOSRES_LIPID -DPOSRES > -DPOSRES_WATER ; position restrain the protein > > ; Run parameters > > integrator = md ; leap-frog integrator > > nsteps = 50000 ; 2 * 50000 = 100 ps > > dt = 0.002 ; 2 fs > > ; Output control > > nstxout = 100 ; save coordinates every 0.2 ps > > nstvout = 100 ; save velocities every 0.2 ps > > nstenergy = 100 ; save energies every 0.2 ps > > nstlog = 100 ; update log file every 0.2 ps > > ; Bond parameters > > continuation = no ; first dynamics run > > constraint_algorithm = lincs ; holonomic > constraints > > constraints = all-bonds ; all bonds > (even heavy atom-H bonds) constrained > > lincs_iter = 1 ; accuracy of LINCS > > lincs_order = 4 ; also related to > accuracy > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cels > > nstlist = 5 ; 10 fs > > rlist = 1.2 ; short-range neighborlist cutoff > (in nm) > > rcoulomb = 1.2 ; short-range electrostatic > cutoff (in nm) > > rvdw = 1.2 ; short-range van der Waals cutoff > (in nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh Ewald for > long-range electrostatics > > pme_order = 4 ; cubic interpolation > > fourierspacing = 0.16 ; grid spacing for FFT > > ; Temperature coupling is on > > tcoupl = V-rescale ; modified > Berendsen thermostat > > tc-grps = Protein_LMT POPC Water_and_ions ; > three coupling groups - more accurate > > tau_t = 0.1 0.1 0.1 ; time constant, in > ps > > ref_t = 271 271 271 ; reference > temperature, one for each group, in K > > ; Pressure coupling is off > > pcoupl = no ; no pressure coupling in NVT > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > ; Dispersion correction > > DispCorr = EnerPres ; account for cut-off vdW > scheme > > ; Velocity generation > > gen_vel = yes ; assign velocities from Maxwell > distribution > > gen_temp = 271 ; temperature for Maxwell > distribution > > gen_seed = -1 ; generate a random seed > > ; COM motion removal > > ; These options remove motion of the > protein/bilayer relative to the solvent/ions > > nstcomm = 1 > > comm-mode = Linear > > comm-grps = Protein_LMT_POPC Water_and_ions > > > > > Please help me...!!!! > > > > > -- > *Padmani sandhu* > *Research Scholar,* > *Center for Computational Biology and Bioinformatics,* > *Central University of Himachal Pradesh,* > *Temporary Academic Block, Shahpur * > *Pin 176206, District Kangra,* > *Himachal Pradesh, India* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.