Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K
At this temperature, it is known by previous literature survey that protein keeps its secondary structure almost intact. But according to my simulations (done thrice), protein starts loosing its secondary structure around 6-8ns only. I have used the following parameters: *em.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 250000 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no *pr.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50000 ; total 100 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Pressure coupling is not on Pcoupl = no 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 *full.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 25000000 ; total 50000 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 I don't think it is the problem of thermostat because even after using V-rescale for temperature coupling and Parinello Rahman for pressure coupling, my protein loses its secondary structure in the initial time of simulation. Also, I have carried out various checks (like potential energy convergence after em, temperature check after pr, and pressure and density check after full), all of which seems to converge well. Please help me figure out the problem. -- 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.
