if I set pbc=xyz in energy minimization mdp file then I get following error
ERROR: can only have neighborlist cut-off zero (=infinite) with coulombtype = Cut-off or coulombtype = User and simple neighborsearch without periodic boundary conditions (pbc = no) and rcoulomb and rvdw set to zero ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. Nilesh On Thu, May 19, 2011 3:57 pm, Vitaly Chaban wrote: >> the equlibration file I used >> >> title = cpeptid position restraining cpp >> = /usr/bin/cpp >> constraints = none integrator = md dt >> = 0.001 ; ps ! >> nsteps = 1000000 ; total 1.0 ps. nstcomm = >> 1 >> nstxout = 10000 nstvout = 10000 nstfout >> = 0 >> nstlog = 10 nstenergy = 10 nstlist = >> 10 >> ns_type = simple comm_mode = none coulombtype >> = cut-off >> vdwtype = cut-off rlist = 0.0 rcoulomb >> = 0.0 >> rvdw = 0.0 pbc = no fourierspacing = >> 0.12 >> fourier_nx = 0 fourier_ny = 0 fourier_nz >> = 0 >> pme_order = 4 ewald_rtol = 1e-5 optimize_fft = >> yes ; Berendsen temperature coupling is on >> Tcoupl = nose-hoover >> tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on >> Pcoupl = NO ;Parrinello-Rahman >> pcoupltype = isotropic tau_p = 2.0 compressibility >> = 4.5e-5 >> ref_p = 1.0 ; Generate velocites is on at 300 K. >> gen_vel = yes gen_temp = 298.0 gen_seed >> = 173529 >> >> >> Is ther any thing wrong with my mdp files. >> WHy they is so much change is cooridnates in the .pdb file. >> >> > > > > Nilesh: > > > Set periodic conditions. This will restrict the coordinates to small > numbers. > > > -- > Dr. Vitaly V. Chaban, Department of Chemistry > University of Rochester, Rochester, New York 14627-0216 > -- > 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 > > > -- 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