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