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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Using heavy hydrogens slows down your dynamics and therefore your sampling.<br>The virtual site hydrogen are used to removal the (fast) angle vibrations involving<br>hydrogens. For the hydrogens you mention the angles will be constrained<br>with option -vsite h, or are already constrained (in water).<br>The fastest degrees of freedom will be dihedrals involving hydrogens.<br>For 4 fs you do not need heavy hydrogens.<br>To go beyond 4 fs you might need heavy hydrogens (although 5 fs might still work),<br>but then you want them all heavy.<br></div>But at 5 or more fs you might start introducing inaccuracies in the integration<br>of degrees of freedom of heavy atoms as well.<br><br>Berk<br><br><br><hr id="stopSpelling">> Date: Thu, 30 Oct 2008 12:38:31 -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>> Thanks Berk,<br>> <br>> My current application is for replica exchange, from which I can not <br>> extract any dynamic information regardless of heavy hydrogens.<br>> <br>> I was under the impression that, when including a protein in the system, <br>> one would generally desire -vsite to apply to everything except "water <br>> and in hydroxyl, sulfhydryl or amine groups", which would utilize heavy <br>> hydrogens. This is based on v4 of the manual, section 6.5, page 125:<br>> <br>> "For the hydrogens in water and in hydroxyl, sulfhydryl or amine groups, <br>> no degrees of freedom can be removed, because rotational freedom should <br>> be preserved. The only other option available to slow down these <br>> motions, is to increase the mass of the hydrogen atoms at the expense of <br>> the mass of the connected heavy atom."<br>> <br>> So, would I then use<br>> <br>> dt = 0.004<br>> constraints = all-bonds<br>> constraint_algorithm = lincs<br>> lincs-iter = 1<br>> lincs-order = 6<br>> <br>> after pdb2gmx -vsite -heavyh<br>> <br>> or would this make all of my hydrogens heavy, even the ones that are <br>> already handled by -vsite?<br>> <br>> Thanks,<br>> Chris.<br>> <br>> <br>> >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>> >I always use 4 fs time steps for my ion-water systems and see no <br>> differences<br>> >with 2 fs simulations in extremely accurate rdf's.<br>> ><br>> >I would use lincs_order=6<br>> ><br>> >> Date: Wed, 29 Oct 2008 22:32:25 -0400<br>> >> From: chris.neale at utoronto.ca<br>> >> To: gmx-users at 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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