Seems like you're using cut-off electrostatics, which would be a good way of picking lottery numbers, and that's about all.
Mark On Mon, Feb 17, 2014 at 10:16 AM, Nidhi Katyal <nidhikatyal1...@gmail.com>wrote: > 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. > -- 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.