Dear gromacs users I have performed the vacuum simulation of protein. The structure was minimized after generating the box using the following mdp parameters. ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = hbonds integrator = steep nsteps = 3000 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01
nstcomm = 1 ns_type = simple rlist = 0.0 coulombtype = cut-off rcoulomb = 0.0 rvdw = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no PBC = no gen_vel = no then i have run the full md for 5ns. mdp parameter are as follows: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 2500000 ; total 5000 ps. nstcomm = 1 nstxout = 500000 nstvout = 500000 comm-mode = ANGULAR lincs_iter = 2 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 500 xtc-precision = 1000 nstlist = 10 ns_type = simple rlist = 0.0 coulombtype = cut-off rcoulomb = 0.0 rvdw = 0.0 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 = no tc-grps = Protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on Pcoupl = no Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 PBC = no Is this a right way to perform the MD in vacuum? Anyone if familiar with this procedure, please suggest. Thanks in Advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.