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>