Dear Gromacs Users, I wonder if it is normal for a protein to move out of the box during MD runs. periodic boundary conditions are applied. system is neutralized. 0.9nm for the distance between box side and protein.
thanks the md.mdp for your reference: title = trp-Cage cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.002 ; ps ! nsteps = 2500000 ; total 5000 ps. nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 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 in two groups Tcoupl = berendsen tau_t = 0.1 tc_grps = system ref_t = 498 ; Pressure coupling is on Pcoupl = berendsen 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 _______________________________________________ gmx-users mailing list [email protected] http://www.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
