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Hi,<br><br>I would expect nearly any cell to deform to a very elongated shape,<br>unless it contains a solid (crystal). In most cases an elongated<br>shape has the lowest (electrostatic) energy. Therefore anisotropic<br>coupling is only useful for crystal simulations.<br><br>Berk<br><br>> Date: Mon, 1 Mar 2010 10:09:08 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Constraining periodic cell<br>> <br>> On 2010-03-01 09.49, David Chalmers wrote:<br>> > David,<br>> ><br>> > I get a different simulation result if I use isotropic or anisotropic cells.<br>> > I am not sure yet which is (more) correct, but I would like to be able to<br>> > run both types to see. I understand that a constrained anisotropic cell is<br>> > not completely anisotropic, but a fully anistropic one clearly doesn't work.<br>> ><br>> > David<br>> <br>> You did not say which algorithm you use either, but making the time <br>> constant longer might help. However, depending on your system, you may <br>> need substantial surface tension to keep the system neutral if you do <br>> use anisotropic coupling. We do not completely understand these effects <br>> yet, see e.g http://bugzilla.gromacs.org/show_bug.cgi?id=165 for <br>> additional discussions.<br>> ><br>> ><br>> >>> Dear All,<br>> >>><br>> >>> We are running some simulations using an anisotropic periodic cell. We are<br>> >>> getting 'cell runaway' with the cell becoming very long and thin. This<br>> >>> appears to being driven by the electrostatics of the system. The simulation<br>> >>> then dies because the smallest cell dimension is less than 2*cutoff.<br>> >>><br>> >>> Is there a way that we can apply some constraints to the periodic cell?<br>> >> Why not use isotropic pressure coupling?<br>> >><br>> >>><br>> >>> Regards<br>> >>><br>> >>> David<br>> ><br>> > ________________________________________________________________________<br>> ><br>> > David Chalmers Lab: 9903 9110<br>> > Faculty of Pharmacy, Monash University<br>> > 381 Royal Pde, Parkville, Vic 3053. Australia<br>> > David.Chalmers@pharm.monash.edu.au<br>> > ________________________________________________________________________<br>> ><br>> ><br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>> spoel@xray.bmc.uu.se http://folding.bmc.uu.se<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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 />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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