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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> From: X.Periole@rug.nl<br>> Subject: Re: [gmx-users] Implicit solvent & PBC<br>> To: gmx-users@gromacs.org<br>> Date: Fri, 19 Sep 2008 17:03:08 +0200<br>> <br>> On Fri, 19 Sep 2008 16:49:45 +0200<br>> Berk Hess <gmx3@hotmail.com> wrote:<br>> > <br>> > <br>> > <br>> > <br>> >> From: X.Periole@rug.nl<br>> >> Subject: Re: [gmx-users] Implicit solvent & PBC<br>> >> To: gmx-users@gromacs.org<br>> >> Date: Fri, 19 Sep 2008 16:42:15 +0200<br>> >> <br>> >> On Fri, 19 Sep 2008 15:00:18 +0200<br>> >> Berk Hess <gmx3@hotmail.com> wrote:<br>> >> > Hi,<br>> >> > <br>> >> > The same as in normal simulations.<br>> >> > I always use PME and PBC in my implicit solvent simulations.<br>> >> then -<br>> >> PME: treament of long range electrostatic interactions in implicit solvent?<br>> >> PBC: simulate infinite dilution again in implicit solvent?<br>> >> <br>> >> I really do not see the point!<br>> > <br>> > I have for instance systems with ions in implicit solvent.<br>> > Since ions have long range electrostatic interactions, you need <br>> > PME (and PBC).<br>> Then of course. I actually thought that might be your case. Is it<br>> actually worth? Are they behaving reasonably, not sticking to anything<br>> they meet? How did you parameterize these funny ones?<br><br>If you do everything systematically and correct it does (nearly) exactly what<br>an all-atom simulation does, see:<br>
B. Hess, C. Holm and N. van der Vegt <br>
<b> Modeling Multibody Effects in Ionic Solutions with a Concentration Dependent Dielectric Permittivity </b> <br>
<a href="http://dx.doi.org/10.1103/PhysRevLett.96.147801" target="_blank"> Phys. Rev. Lett. 96, 147801 (2006)</a><br>http://dx.doi.org/10.1103/PhysRevLett.96.147801<br><br>> > Because it is implicit solvent you need to use the appropriate epsilon_r.<br>> > <br>> > I don't see what PBC has to do with infinite dilution.<br>> That is the original idea of using PBC: simulate a molecule in a box of<br>> solvent that would not have boundaries=infinite dilution. The concept has<br>> derived towards "periodic systems" but it is not supposed to be. This is<br>> why I generally do not use PME.<br><br>I don't agree with this.<br>PBC is very useful for crystals.<br>For non-periodic systems PBC is still the best solution,<br>since using any boundary produces more artifacts.<br><br>Electrostatic interactions go as 1/r.<br>A full electrostatics solver, such as PME, is the only way to get the full 1/r.<br>Any other methods does not produce the correct 1/r interaction.<br>If PME produces artefacts, your unit-cell is too small.<br>This is not a problem of PME, but of your system size.<br><br>Berk<br><br>> > <br>> > Berk<br>> > <br>> >> Tsjerk might have a point with crystal packing ...<br>> >> > <br>> >> > Berk<br>> >> > <br>> >> > <br>> >> >> From: X.Periole@rug.nl<br>> >> >> Subject: Re: [gmx-users] Implicit solvent & PBC<br>> >> >> To: gmx-users@gromacs.org<br>> >> >> Date: Fri, 19 Sep 2008 14:52:39 +0200<br>> >> >> <br>> >> >> On Fri, 19 Sep 2008 17:28:20 +0530 (IST)<br>> >> >> Anirban Ghosh <anirbanz83@yahoo.co.in> wrote:<br>> >> >> > Hi All,<br>> >> >> > <br>> >> >> > I am simulating a Coarse Grained model using implicit solvent <br>> >>condition. <br>> >> >>Can <br>> >> >> >Periodic Boundary Condition and Particle-Mesh-Ewald be used with <br>> >>implicit <br>> >> >> >solvent simulation? <br>> >> >> What would be the use of PME and PBC in implicit solvent?<br>> >> >> > Thanks,<br>> >> >> > <br>> >> >> > <br>> >> >> > <br>> >> >> > <br>> >> >> > Anirban Ghosh<br>> >> >> > M.Tech Bioinformatics<br>> >> >> > University of Hyderabad<br>> >> >> > <br>> >> >> > <br>> >> >> > <br>> >> >> > Unlimited freedom, unlimited storage. Get it now, on <br>> >> >> >http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/<br>> >> >> <br>> >> >> -----------------------------------------------------<br>> >> >> XAvier Periole - PhD<br>> >> >> <br>> >> >> Molecular Dynamics Group / NMR and Computation<br>> >> >> University of Groningen<br>> >> >> The Netherlands<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 <br>> >>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>> >> > _________________________________________________________________<br>> >> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> >> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> >> <br>> >> -----------------------------------------------------<br>> >> XAvier Periole - PhD<br>> >> <br>> >> Molecular Dynamics Group / NMR and Computation<br>> >> University of Groningen<br>> >> The Netherlands<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>> > _________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> <br>> -----------------------------------------------------<br>> XAvier Periole - PhD<br>> <br>> Molecular Dynamics Group / NMR and Computation<br>> University of Groningen<br>> The Netherlands<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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