The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md ; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 5000000 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear ; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal
; 7.3.8 Output Control nstxout = 2500000 ; [steps] freq to write coordinates to trajectory nstvout = 2500000 ; [steps] freq to write velocities to trajectory nstfout = 2500000 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps = System ; group(s) to write to xtc trajectory energygrps = System ; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb = 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw >= rlist rvdw = 0.8 ; [nm] distance for LJ cut-off DispCorr = EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = v-rescale ; temperature coupling with Nose-Hoover ensemble tc_grps = Protein Non-Protein ; groups to couple seperately to temperature bath tau_t = 0.1 0.1 ; [ps] time constant for coupling ref_t = 310 310 ; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5 ; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no ; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm = LINCS ; LINear Constraint Solver continuation = yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30 ; [degrees] maximum angle that a bond can rotate before LINCS will complain best regards Urszula Uciechowska > 2015-03-17 14:35 GMT-03:00 Urszula Uciechowska < > urszula.uciechow...@biotech.ug.edu.pl>: > >> >> >> Hi, >> >> I am running MD for dsDNA-protein complex. After 50ns I observed that >> the >> DNA is unwinding. What did go wrong? Should I have changed something in >> my >> input file? >> >> You might want to send your input files, so as your force field that you > have choose. It is hard to say anything without more details. > Also, what do you mean by 'unwinding'? Could you be more specific? > > >> Thank you in advance for your suggestions. >> best regards >> Urszula >> > > Cheers! > -- > Marcelo Depólo Polêto > B.Sc. Biochemistry - University of Viçosa (Brazil) > -- > 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. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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.