....Insert another protein and press ENTER... 1. Try energy minimization before MD. 2. Remove constraints temporarily.
What will be the result? Dr. Vitaly Chaban > On running, Molecular dynamics simulation of protein-protein complex, While > running md run, i got this error, > * > "Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5# > > Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5# > > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.011042, max 4.472447 (between atoms 12 and 14) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > > Back Off! I just backed up step0b.pdb to ./#step0b.pdb.15# > > Back Off! I just backed up step0c.pdb to ./#step0c.pdb.15# > - Show quoted text - > > Wrote pdb files with previous and current coordinates > > I used this parameter file:* > > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 10000 ; total 20.0 ps. > nstcomm = 1 > nstxout = 250 ; collect data every 0.5 ps > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.4 > fourierspacing = 0.135 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > DispCorr = no > ; Berendsen temperature coupling is on > Tcoupl = v-rescale > tau_t = 0.1 0.1 > tc-grps = protein non-protein > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = parrinello-rahman > Pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > Can u help me in, how to rectify this problem and find a suitable solution > to the problem. > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
