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Hi,<br><br>I don't think it matters much if you put the cut-off at a minimum in the rdf.<br>The real issue is that the force is not updated beyond the cut-off,<br>while the atoms there still move. You want as little motion,<br>of better as little change in force due to the motion of the atoms<br>as possible. The solution to this is to increase the cut-off as much<br>as possible, but this is computationally unfavourable.<br><br>I should also note the all versions of Gromacs up till now use<br>a very simplistic twin-cut off setup with an integrator which<br>is not reversible. This can lead to significant energy increase in the system.<br>Therefore twin-range cut-off should not be used for Coulomb interactions,<br>only for Lennard-Jones, where the forces are anyhow very small.<br>We might consider implementing a proper multiple time step integrator for<br>version 4.1 or 4.2.<br><br>Berk<br><br>> Subject: Re: [gmx-users] Twin range cut-off's: rlist and rvdw<br>> From: jussi.lehtola@helsinki.fi<br>> To: gmx-users@gromacs.org<br>> Date: Wed, 27 May 2009 16:05:25 +0300<br>> <br>> 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>> 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.<br>> <br>> > Do people think the effect of these inward moving and outward moving<br>> > particles is small and the error for calculation can be tolerated?<br>> <br>> When particles move in and out of the cutoff range it induces static in<br>> the properties. Ideally for monocomponent systems (such as metals) the<br>> cutoff should be in an (absolute) minimum of the pair correlation<br>> function, i.e. there aren't many particles in the region where the<br>> cutoff is made. For molecular systems the decision of a cutoff is<br>> harder, since some pair correlations stay quite constant and there is no<br>> clear cut way to make the decision.<br>> <br>> The farther you go the fewer static you get. Roughly speaking, the<br>> number of particles at cutoff range grows as r_cut^2, but for<br>> Lennard-Jones the interaction weakens as r_cut^-6, resulting in an error<br>> proportional to r_cut^-4.<br>> -- <br>> ------------------------------------------------------<br>> Jussi Lehtola, FM, Tohtorikoulutettava<br>> Fysiikan laitos, Helsingin Yliopisto<br>> jussi.lehtola@helsinki.fi, p. 191 50632<br>> ------------------------------------------------------<br>> Mr. Jussi Lehtola, M. Sc., Doctoral Student<br>> Department of Physics, University of Helsinki, Finland<br>> jussi.lehtola@helsinki.fi<br>> ------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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