Hi Tsjerk,<br><br>Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very clear about the parameters used in mdp files. So I am sending the mdp file here. <br>
<br><br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 500000 ; total 1000 ps.<br>nstcomm = 1<br>
nstxout = 500 ; collect data every 1 ps<br>nstvout = 0<br>nstfout = 0<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>
rcoulomb = 1.0<br>vdwtype = Cut-off<br>rvdw = 1.4<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>; Berendsen temperature coupling is on<br>Tcoupl = V-rescale<br>tau_t = 0.1 0.1<br>tc_grps = Protein SOL<br>
ref_t = 300 300<br>; Pressure coupling is on<br>Pcoupl = Parrinello-Rahman<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br><br>