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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Tue, 4 Nov 2008 10:48:16 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] RE: vsite problem in gromacs 4.0<br>> <br>> 1) Are whole charge groups are utilized also for LJ calculation if one <br>> atom of that charge group falls within the cutoff? If so, it seems to <br>> me that putting all of the atoms in each aromatic side chain into <br>> their own charge group could slightly change the equilibrium <br>> properties of a peptide or protein since aromatic residues would then <br>> be more strongly attracting near the cutoff distance than they are <br>> when assigned the regular charge groups of a force-field. Probably not <br>> a serious issue, but something to consider.<br><br>Most force fields (except GROMOS) have probably been parametrized<br>without charge groups.<br>Therefore having smaller charge groups is always more accurate, unless you<br>have a buffer region, which is now possible in 4.0. (This all assumes that<br>you use PME and not cut-off or reaction-field for electrostatics)<br>This is indeed not a serious issue.<br><br>> <br>> 2) Also, Berk, you mention the possibility for "dt=4 or 5 fs with <br>> -vsite h (and optionally heavy hydrogens)". I am a little confused <br>> again. I interpreted, based on some help that you gave me last week, <br>> that the following should be enough:<br>> <br>> pdb2gmx -vsite, with:<br>> dt = 0.004<br>> constraints = all-bonds<br>> constraint_algorithm = lincs<br>> lincs-iter = 1<br>> lincs-order = 6<br>> <br>> And that to go above dt=0.005 would require heavy hydrogens also, <br>> although that might not be such a good idea.<br><br>Using 5 fs without heavy hydrogens will not cause stability problems.<br>It might cause slightly less accurate integration. But these integration<br>errors are usually much smaller than other errors, such as cut-off errors.<br>It is all a matter of what accuracy you want.<br>If you want to be sure, you can run simulations with a 4 and 5 fs timestep<br>(do not forget to modify nstlist as well, so the neighborlist update frequency<br>stays constant) and then check if the properties you are interested in change.<br>For many properties this might not be feasible, since you can not converge<br>the properties within reasonable time.<br><br>In our experience 5 fs works fine. I would not hesitate to use it for large<br>systems, where one can anyhow not sample all conformational space.<br>I am currently mainly doing accurate calculations of thermodynamic quantities,<br>for these I use 4 fs.<br><br>Berk<br><br>> <br>> your post: http://www.gromacs.org/pipermail/gmx-users/2008-October/037569.html<br>> <br>> Thanks for any clarifications,<br>> Chris.<br>> <br>> <br>> <br>> -- original message --<br>> <br>> You can not do much.<br>> The reason for this error message is also valid for older versions.<br>> It can not be guaranteed that the virtual sites in one charge group will<br>> have the same periodic shift. But before 4.0 there was no check for this.<br>> <br>> I would simply not use vsite aromatics. I am in favor of completely<br>> removing this option from pdb2gmx, since you do not gain so much<br>> compared with dt=4 or 5 fs with -vsite h (and optionally heavy hydrogens).<br>> <br>> If you really want to use the vsite aromatics, you can put all atoms<br>> in the aromatic groups in separate charge groups, but that will make<br>> the simulation slightly slower.<br>> <br>> Berk<br>> <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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