<div class="gmail_quote">On Wed, May 27, 2009 at 3:05 PM, Jussi Lehtola <span dir="ltr"><<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On Wed, 2009-05-27 at 14:33 +0200, Yan Chai wrote:<br>
<br>
> It seems that in the twin range cut-off method, rlist does not only<br>
> play a role as a cut-off for neighbor searching, but also as a cut-off<br>
> for short-range interactions. Do I understand correctly?<br>
<br>
</div>If you're using Coulombic cutoffs, then yes. If you're using PME, then<br>
AFAIK the part r > rcut will be performed in Fourier space.</blockquote><div><br>Excuse me, to make sure whether my understanding is correct or not, might I check the following two examples?<br><br> Case 1, let's consider PME and set rlist=rcoulomb. At time t=0, there are a particle O at the original point, a outward moving particle A within the radius of rlist=rcoulomb, and a inward moving particle B out of the radius of rlist=rcoulomb, as shown below<br>
<br> O -- A -- rlist -- B, for t=0<br><br> I set nstlist=10. At t=0, the neighborlist of particle O is created and particle A is on the list but particle B is not. The Coulomb forces on particle O is also calculated, and F_OA is calculated in real space while F_OB is calculated in Fourier space:<br>
<br> Fcoulomb=Fcoulomb_OA_real+Fcoulomb_OB_fourier, for t=0.<br><br> Let's imagine when the time is between t=0 and t=10, before the second time for neighborlist update, particle A moves outside of the radius of rlist=rcoulomb and particle B moves inside of the radius of rlist=rcoulomb, as shown below<br>
<br> O -- B -- rlist -- A, for 0<t<nstlist<br><br> Now particle A is still on the neighborlist of particle O and particle B is still not. I would expect that Gromacs will calculate the Coulomb interaction to particle O by particle A twice: once in the real space because particle A is on the neighborlist of particle O, and the other one at the same time in Fourier space because particle is outside of the radius rcoulomb. On the other hand, there will be no account for the Coulomb interaction to particle O by particle B because particle B is neither on the list of O nor outside of rcoulomb. <br>
<br> Fcoulomb=Fcoulomb_OA_real+Fcoulomb_OA_fourier, for 0<t<nstlist.<br><br> <br> Case 2, let's consider van der Waals interaction and set rlist<rvdw. Similar to Case 1, we have particles which shift the positions as below:<br>
<br> O -- A -- rlist -- B -- rvdw, for t=0<br><br> O -- B -- rlist -- A -- rvdw, for 0<t<nstlist<br><br> I would expect that during 0<t<nstlist, the van der Waals force applied on particle O will be<br>
<br> Fvdw=Fvdw_OA(0<t<nstlist)+Fvdw_OB(t=0), for 0<t<nstlist<br><br> which means that particle A can apply van der Waals force on particle O even if particle A is beyond rlist since particle A is still on the neighborlist of particle O.<br>
<br> Do I understand correctly for these two cases above?<br><br> Thanks!<br><br> Yan<br><br><br> <br></div></div><br>