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<br><br>> Date: Fri, 8 May 2009 19:38:41 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] (no subject)<br>> <br>> Antonia V. wrote:<br>> > Dear all,<br>> > <br>> > I am trying to simulate a water-liquid crystal system. My initial is box <br>> > is creating by merging two well equilibrated boxes of water and LC. <br>> > After a steep simulation of about 1,000,000 steps I try to do an md <br>> > simulation but I get the error<br>> > "Water molecule starting at atom 9103 can not be settled.<br>> > Check for bad contacts and/or reduce the timestep"<br>> > In order to get the simulation running I have to use a tiny timestep <br>> > (0.00001).<br>> <br>> Have a look at the region around atom 9103 in case you can deduce a <br>> physical reason for large forces that would make applying constraints <br>> difficult.<br>> <br>> Otherwise, consider alternative approaches to generating your initial <br>> structure. It's not clear to me that whatever you mean by "merging" is <br>> reasonable.<br>> <br>> Mark<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 />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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