Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K
Does it make sense? The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3. Thank you Lin ; VARIOUS PREPROCESSING OPTIONS title = Lysozyme cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 250000 ; 500 picoseconds total simulation time comm_mode = Linear ; Removing overall translations from the system nstcomm = 1 ; ... and doing so every step ; OUTPUT CONTROL OPTIONS nstxout = 1000 ; Writing full precision coordinates every nanosecond nstvout = 0 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 0 ; Writing to the log file every step nstenergy = 1000 ; Writing out energy information every step nstxtcout = 1000 ; Writing coordinates every step xtc_precision = 1000 ; Floating point number to integer scaling xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 300.0 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php