Hi,<br>I've been using gromacs to run some tests but it's the first time I need to heat my system very slowly, knowing that it is a quite large system.<br><br>;<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>
; Input file<br>;<br>title = Yo<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>constraint_algorithm = Lincs<br>lincs_iter = 2<br>integrator = md<br>dt = 0.002 ; ps !<br>
nsteps = 225000 ; total 450 ps.<br>nstcomm = 1<br>nstxout = 250 ; collect data every 0.5 ps<br>nstvout = 500 ; collect velocities every 1 ps<br>nstfout = 0<br>
nstlog = 50<br>nstenergy = 50 ; collect energies every 0.1 ps<br>nstlist = 10<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>
vdwtype = cut-off<br>rvdw = 1.2<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br>annealing = single single<br>annealing_npoints = 10 10<br>annealing_time = 0 100 105 200 202 250 252 350 355 450 0 100 105 200 202 250 252 350 355 450<br>annealing_temp = 50 50 100 100 150 150 200 200 300 300 50 50 100 100 150 150 200 200 300 300<br>
; Berendsen temperature coupling is on in two groups<br>Tcoupl = Berendsen<br>tc-grps = Protein Non-protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Energy monitoring<br>
energygrps = Protein Non-protein<br>; Isotropic pressure coupling is now on<br>Pcoupl = no<br>Pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
; Generate velocites is off at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>Please can anyone tell me if my mdp file is correct? I have a serious doubt about gen_temp & Tcoupling.<br>
<br>Thanks<br>Carla<br>