Hello, I used a -maxwarn 5, but I only obtain 1 warning, (about obsolete entries that the .mdp file has). I used a solute-box distance of 0.34 in order to reduce the simulation box. I used before a solute-box distance of 1 nm and the problem persist.
my .mdp file is the next: ; VARIOUS PREPROCESSING OPTIONS title = cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.004 nsteps = 2 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10000 nstvout = 10000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 100 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1.2 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1.4 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.24 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc-grps = protein sol ; Time constant (ps) and reference temperature (K) tau-t = 0.1 0.1 ref-t = 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 compressibility = 5e-5 ref-p = 1 ; Random seed for Andersen thermostat andersen_seed = 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = yes ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no Thanks in advance, Luis Miguel Medina Solano wrote: Hello, I'm very sorry for the way I reply, the truth is that i didn't know how else to reply (it is my first time posting here).the script to generate the REMD is: #!/bin/bash # ff opsla and water spc # echo -e "14\n4\n3\n3 0" |pdb2gmx -f 1.pdb -o inib4em.pdb -p topol.top -ignh -tereditconf -f inib4em.pdb -o inib4em.pdb -d 0.34 -bt dodecahedron Using a solute-box distance of only 0.34 nm is probably unwise. Why have you chosen such a short distance?grompp -v -f iniem.mdp -o em -c inib4em.pdb -maxwarn 5 Why are you using -maxwarn, especially to ignore up to five errors? The notes that grompp prints are helpful in that they usually indicate sources of instability in your system by way of algorithm conflict.mdrun -v -s em -c ini_after_em.pdb -deffnm ini_after_em editconf -f ini_after_em.pdb -o ini_after_em.pdb -d 0.34 -bt dodecahedrongenbox -cp ini_after_em.pdb -cs spc216 -o sol_b4em.pdb -p topol.top grompp -v -f em.mdp -c sol_b4em.pdb -o sol_em -p topol.top -maxwarn 5 mdrun -v -s sol_em -c sol_after_em.pdb -deffnm sol_after_em grompp -v -f rp.mdp -c sol_after_em.pdb -o sol_rp -p topol.top -maxwarn 5 mdrun -v -s sol_rp -c sol_after_rp.pdb -deffnm sol_after_rp # NVT and NPT runs for each replica for ((i = 0; i<= 42 ; i ++)) do grompp -v -f nvt$i.mdp -c sol_after_rp.pdb -o sol_nvt$i -p topol.top -maxwarn 5mdrun -v -s sol_nvt$i.tpr -c sol_after_nvt$i.pdb -deffnm sol_after_nvt$i grompp -v -f npt$i.mdp -c sol_after_nvt$i.pdb -o sol_npt$i -p topol.top -maxwarn 5mdrun -v -s sol_npt$i.tpr -c sol_after_npt$i.pdb -deffnm sol_after_npt$i editconf -f sol_after_npt$i.pdb -o sol_after_nptt$i.pdb -c grompp -v -f solv$i.mdp -c sol_after_nptt$i.pdb -o sol_solv$i -p topol.top -maxwarn 5Providing your .mdp files is probably useful for determining the source of your problems, but more likely either (or both) of the above points will have critical clues.-Justin done # REMD run mpiexec -l -np 43 mdrun_mpi -v -s sol_solv.tpr -multi 43 -replex 500 -c Folded.pdb -deffnm FoldedBest regards -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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