> 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
