1)I use steepest to minimize energy, .mdp as follows, title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = all-bonds integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep =0.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529
2) then I use cg do energy minimization, .mdp as follows, title = bovin cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = cg dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes emtol = 100.0 emstep = 0.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 both constraint all bond, 1) steepest is no problem; but 2) some error take place at cg I use grompp_d -f em_cg_constrain.mdp -c em.pdb -p topol.top -o bovin_em_cg.tpr mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg Starting 16 threads, ........... Fatal error: DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. at em_cg.log , maximum distance required for P-LINCS: 0.876 nm So, I revised the mdrun, mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg -nt 2 -rcon 0.876 nm -dds 0.876 another error take place, Fatal error: Too many LINCS warnings (1011) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem So, is anyway to resolve it ? I have try, but can not find the way. Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/cg-Fatal-error-DD-cell-tp5008859.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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