> > Hi > I used Gromacs version 3.3.3. > My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 > ) > MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total > After doing the energy minimization, => the potential energy is extremely > high ( say, ten to the 9th order ) > I visualized the " Simulation-System-EM-solvated.gro " after the energy > minimization. > Then, I found that the Simulation Sysmtem is devided into 16 domains very > clearly and the molecules (protein, ligand, and water) break into atoms in > the boundaries. > I have checked that the 20 ligands are not overlapped each other and are > not > overlapped with protein from the beginning. > > > > More, i have created 10 alike system and each is with "one protein + 20 > ligand + water molecules" > Two of them get the "minus potential energy" after energy minimization and > I > can continue running the MD simulation successfully. > Others of them get the "extreme high positive potential energy" and the > system is devided into 16 domains after energy minimization and the > simulation broke afterall. > > > > With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 ) > There is no problems like that. > > > Please give me your ideas to solve the problem. > > The commands are listed below and the .tpr file created by grompp is > attached. > > > > Thank you > Lin > > > > > > ** > 1. pdb2gmx_mpi -f 6LYZ.pdb -o 6LYZ.gro -p 6LYZ.top => G 45a3 > > 2. Energy minimization of the structure (vacuum) > > pbc = no, > > grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o > 6LYZ-EM-vacuum.tpr > > mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum > > > > > > 3. Periodic boundary conditions > > editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box > 7.0 7.0 7.0 > > > > *4. Add another 20 ligands randomly into the* *simulation (nm^3) box* > > genbox_mpi -seed 201 -cp 6LYZ-PBC.gro -ci ligand.gro -nmol 20 -p 6LYZ.top -o > 6LYZ20ligand.gro > > > > *6. Solvent addition* > > genbox_mpi -cp 6LYZ20ligand.gro -cs spc216.gro -p 6LYZ.top -o > 6LYZ-water.gro > > > > *7. Addition of ions: counter charge and concentration* > > grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr > > genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 28 -nname CL- > > > > *8. Energy minimization of the solvated system* > > pbc = xyz (minim.mdp) > > grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o > 6LYZ-EM-solvated > > mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated > > > > >
> > Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision) > Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision) > 6LYZ-EM-solvated.tpr: > header: > bIr = present > bBox = present > bTop = present > bX = present > bV = present > bF = not present > natoms = 33042 > step = 0 > t = 0.000000e+00 > lambda = 0.000000e+00 > ir: > integrator = steep > nsteps = 50000 > init_step = 0 > ns_type = Simple > nstlist = 5 > ndelta = 2 > bDomDecomp = FALSE > decomp_dir = 0 > nstcomm = 1 > comm_mode = Linear > nstcheckpoint = 1000 > nstlog = 100 > nstxout = 100 > nstvout = 100 > nstfout = 0 > nstenergy = 1 > nstxtcout = 0 > init_t = 0 > delta_t = 0.001 > xtcprec = 1000 > nkx = 0 > nky = 0 > nkz = 0 > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 0 > epsilon_surface = 0 > optimize_fft = FALSE > ePBC = xyz > bUncStart = FALSE > bShakeSOR = FALSE > etc = No > epc = No > epctype = Isotropic > tau_p = 1 > ref_p (3x3): > ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compress (3x3): > compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > andersen_seed = 815131 > rlist = 1 > coulombtype = Cut-off > rcoulomb_switch = 0 > rcoulomb = 1 > vdwtype = Cut-off > rvdw_switch = 0 > rvdw = 1 > epsilon_r = 1 > epsilon_rf = 1 > tabext = 1 > gb_algorithm = Still > nstgbradii = 1 > rgbradii = 2 > gb_saltconc = 0 > implicit_solvent = No > DispCorr = No > fudgeQQ = 1 > free_energy = no > init_lambda = 0 > sc_alpha = 0 > sc_power = 0 > sc_sigma = 0.3 > delta_lambda = 0 > disre_weighting = Conservative > disre_mixed = FALSE > dr_fc = 1000 > dr_tau = 0 > nstdisreout = 100 > orires_fc = 0 > orires_tau = 0 > nstorireout = 100 > dihre-fc = 1000 > dihre-tau = 0 > nstdihreout = 100 > em_stepsize = 0.01 > em_tol = 1 > niter = 20 > fc_stepsize = 0 > nstcgsteep = 1000 > nbfgscorr = 10 > ConstAlg = Lincs > shake_tol = 0.0001 > lincs_order = 4 > lincs_warnangle = 30 > lincs_iter = 1 > bd_fric = 0 > ld_seed = 1993 > cos_accel = 0 > deform (3x3): > deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > grpopts: > nrdf: 99123 > ref_t: 0 > tau_t: 0 > anneal: No > ann_npoints: 0 > acc: 0 0 0 > nfreeze: N N N > energygrp_flags[ 0]: 0 > efield-x: > n = 0 > efield-xt: > n = 0 > efield-y: > n = 0 > efield-yt: > n = 0 > efield-z: > n = 0 > efield-zt: > n = 0 > bQMMM = FALSE > QMconstraints = 0 > QMMMscheme = 0 > scalefactor = 1 > qm_opts: > ngQM = 0 > box (3x3): > box[ 0]={ 7.00000e+00, 0.00000e+00, 0.00000e+00} > box[ 1]={ 0.00000e+00, 7.00000e+00, 0.00000e+00} > box[ 2]={ 0.00000e+00, 0.00000e+00, 7.00000e+00} > boxv (3x3): > boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > pcoupl_mu (3x3): > pcoupl_mu[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} > pcoupl_mu[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} > pcoupl_mu[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} > nosehoover_xi: 0 > x (33042x3): > x[ 0]={ 3.88200e+00, 2.44200e+00, 2.61100e+00} > x[ 1]={ 3.87900e+00, 2.34300e+00, 2.62700e+00} > x[ 2]={ 3.97600e+00, 2.47000e+00, 2.59300e+00} > x[ 3]={ 3.85000e+00, 2.49000e+00, 2.69300e+00} > x[ 4]={ 3.79500e+00, 2.47800e+00, 2.49600e+00} > x[ 5]={ 3.65000e+00, 2.43700e+00, 2.52700e+00} > x[ 6]={ 3.55300e+00, 2.46400e+00, 2.41200e+00} > x[ 7]={ 3.41000e+00, 2.42200e+00, 2.44600e+00} >
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