Dear gromacs users, I am trying to simulate a 225aa protein at 300K in water, with OPLSAA force filed, tip4p water model, using the parameters below (for pressure equilibration) during position restrained md.
integrator = md dt = 0.002 nsteps = 50000 nstcomm = 10 nstlist = 5 ns_type = grid pbc = xyz rlist = 1.40 coulombtype = PME rcoulomb = 1.40 vdwtype = Switch rvdw_switch = 0.9 rvdw = 1.00 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = nose-hoover tc_grps = Protein Non-Protein tau_t = 0.4 0.4 ref_t = 300 300 nh-chain-length = 1 gen_vel = no continuation = yes constraints = all-bonds constraint-algorithm = LINCS lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 when I calculate the densities, the average came out to be 1025.91 kg/m^3, Could anyone please clarify me the reason for this density. Thanking you With regards Kavya
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