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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Just use:<br>pdb2gmx -vsite h<br>and use LINCS with all bonds constrained<br>I would use lincs_order=6 with dt=4 fs, see the P-LINCS paper for details:<br>http://dx.doi.org/10.1021/ct700200b<br><br>I would not use heavy hydrogen, since that affects the dynamics.<br></div>I always use 4 fs time steps for my ion-water systems and see no differences<br>with 2 fs simulations in extremely accurate rdf's.<br><br>I would use lincs_order=6<br><br><hr id="stopSpelling">> Date: Wed, 29 Oct 2008 22:32:25 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] 4fs timestep in gromacs 4.0<br>> <br>> Hello,<br>> <br>> I am interested in trying the 4 fs timestep options for an <br>> opls-protein/tip4p-water system. I will of course do some quick NVE <br>> tests to ensure that the energy does not drift massively, and also do <br>> some other tests that look at some properties that should equilibrate <br>> rather quickly. Also, I realize that there is no substitute for <br>> reading the literature.<br>> <br>> Still, I am hoping to get some indication of how this was intended to <br>> be utilized in gmx4. Can I just run pdb2gmx -vsite -heavyh and apply <br>> LINCS to all-bonds? The information in the gmx4 manual is nicely <br>> detailed about how each type of hydrogen should be treated, but I am <br>> not clear how to achieve this in my .top.<br>> <br>> Searches for vsite and heavyh reading only the 2008 posts did not give <br>> me much indication about this.<br>> <br>> Thanks,<br>> Chris.<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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