Dear Justin and Mark, I want to investigate the structure xxx.pdb. When I run "the run.mdp" the gromac shows that will end in 25 days. What kind of changes do you recommend in "the run.mdp file" to reduce/short the calculation time? Or, Is there any error/missing in the file? My run.mdp input script is the following.
PC hardware:İntel Core I7 (four core), 6GB RAM Thanks in advance "The run.mdp" title = MD cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000000 ; total 20000 ps = 20 ns. nstcomm = 1 nstxout = 100000 ; collect data every 200 ps nstvout = 100000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein non-protein ; Pressure coupling Pcoupl = berendsen tau_p = 1.0 compressibility = 5e-5 5e-5 5e-5 0 0 0 ref_p = 1.0 -- Ahmet YILDIRIM
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