Hi, I am running simulations using implicit solvent. I am using the pbc = no option in my mdp file, however, I see it the .gro file that gromacs is creating a box for the system.What is the effect of the box in implicit solvent simulations?
This is the mdp file that I am using: ------run.mdp------ integrator = md nsteps = 20000 dt = 0.001 implicit_solvent = GBSA pbc = no nstlist = 0 ns_type = simple rlist = 0 rgbradii = 0 coulombtype = Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 1000 energygrps = Protein_chain_A Protein_chain_C Protein_chain_E Protein_chain_G Protein_chain_I Protein_chain_K gen_vel = yes gen_temp = 1000 ld_seed = -1 gen_seed = -1 nstxout = 1 nstvout = 1 nstxtcout = 1 nstenergy = 1 ------------------ Thanks, Ifat M.Sc. Student Bar Ilan University Ramat Gan Israel
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