Dear Users:<br><br>I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics:<br><br>title = water<br>cpp = /lib/cpp<br>constraints = all_bonds<br>integrator = md<br>
dt = 0.004 ; ps !<br>nsteps = 500000 ; total 8ns.<br>nstcomm = 1<br>nstxout = 50000<br>nstvout = 50000<br>nstfout = 0<br>nstlog = 5000<br>
nstenergy = 5000<br>nstxtcout = 25000<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>coulombtype = Cut-off<br>rlist = 0.8<br>rcoulomb = 0.9<br>
rvdw = 0.8<br>fourierspacing = 0.12<br>ewald_rtol = 1e-5<br>;nemd<br>cos_acceleration = 0.005<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>
tc_grps = SOL<br>tau_t = 0.1<br>ref_t = 300<br>; Energy monitoring<br>energygrps = SOL<br>; Isotropic pressure coupling is now on<br>Pcoupl = berendsen<br>
pcoupltype = isotropic<br>;pc-grps = SOL<br>tau_p = 1.0<br>ref_p = 1.0<br>compressibility = 4.5e-5<br><br>; Generate velocites is off at 300 K.<br>gen_vel = yes<br>
gen_temp = 300.0<br>gen_seed = 100000<br><br clear="all">I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance!<br>
-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>