<br /><br /><span>On 11/10/11, <b class="name">Carla Jamous </b> <carlajamous@gmail.com> wrote:</span><blockquote cite="mid:CADWXoGnVwxkcJjiKRcAJwz9oqUANjQOFiAyfBhRL63ZoLPYAYg@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi everyone,<br /><br />I ran my simulations with these parameters:<br /><br />nstlist = 10<br />ns_type = grid<br />rlist = 0.9<br />coulombtype = PME<br />rcoulomb = 0.9<br />vdwtype = cut-off<br />
rvdw = 1.2<br /><br />Apparently, in Gromacs, when using vdwtype = cut-off,
<style type="text/css">pre.cjk { font-family: "DejaVu Sans",monospace; }p { margin-bottom: 0.21cm; }</style>the potential changes discontinuously.</div></blockquote><br />The potential as a function of distance between any pair of atoms is discontinuous at the cutoff.<br /><br /><blockquote cite="mid:CADWXoGnVwxkcJjiKRcAJwz9oqUANjQOFiAyfBhRL63ZoLPYAYg@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"> However, I have a constant LJ(SR) energy and a constant LJ(LR) energy, </div></blockquote><br />So your particle density is nearly constant. Particles moving inside the cutoff balance those moving outside the cutoff. A changing value should indicate lack of equilibrium, not whether the cut-off is a significant source of error.<br /><br /><blockquote cite="mid:CADWXoGnVwxkcJjiKRcAJwz9oqUANjQOFiAyfBhRL63ZoLPYAYg@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">although I didn't use either Switch or Shift. Please can anyone explain how does the cut-off really works in Gromacs and whether my simulations are correct or not?</div></blockquote><br />Please see the discussions in the manual for theory. Probably the simulations are fine.<br /><br />Mark<br /><blockquote cite="mid:CADWXoGnVwxkcJjiKRcAJwz9oqUANjQOFiAyfBhRL63ZoLPYAYg@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><br />
<br />Thanks<br /><br />Carla<br />
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