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Hi,<br><br>Our philosophy up till now is that with bond constraints and hydrogens<br>replaced by virtual sites one can reach a time step of 4 or 5<br>femtoseconds. This is roughly equal to the largest time step, used for<br>the PME mesh part, in multiple time stepping. But we then do less<br>work on the non-bonded and bonded interactions. Therefore we think<br>that out aproach is somewhat more efficient.<br>But we are thinking about implementing multiple time stepping as well.<br>I already implemented proper reversible multiple time stepping for<br>the typical Gromos twin-range non-bonded force setup for the 4.5<br>release.<br><br>Berk<br><br>> Date: Wed, 30 Jun 2010 01:41:01 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] multiple time step<br>> <br>> I recall seeing something online about how gromacs developers have <br>> decided to focus on increasing the overall speed and allowing <br>> generally large timesteps (via e.g. angle constraints) vs. <br>> implementing multiple timestepping (no mailing list ref. sorry). I <br>> agree that this is not a logically exclusive decision -- PME takes <br>> >20% of the time so if they were doing it only 1/2 as often then <br>> there is the possibility of a real speedup. Nevertheless, it would <br>> need to be tested and perhaps the developers have indeed run these <br>> tests -- I've simply not seen the results. One would think, though, <br>> that PME could nearly always be done less often than, for example, <br>> bonded interactions.<br>> <br>> I agree with Erik that the work would be large, but I disagree that <br>> the benefits would be small -- although I suspect that neither of us <br>> has any data to support such claims :).<br>> <br>> Unfortunately, the bottom line is that this is free software and if <br>> you want it then you can code it. Or at the very least, you should <br>> benchmark the benefits on NAMD and then submit an "enhancement" <br>> bugzilla.<br>> <br>> Chris.<br>> <br>> <br>> -- original message --<br>> <br>> The core developers have the answer for this one, but I can make an<br>> educated guess:<br>> <br>> Implementing it would mean a LOT of work and the rewards are small. The<br>> latter because most particles will have rougly the same oscillation<br>> period if one uses all-atom forcefields and turn on virtual sites and<br>> constrains the bonds, hence the point of having multiple time steps is lost.<br>> <br>> Vitaly Chaban skrev:<br>> > Chris,<br>> ><br>> > An interesting question...<br>> ><br>> > BTW, is there any philosophy of gromacs developers to avoid this<br>> > algorithm in the MD engine?<br>> ><br>> > Vitaly<br>> ><br>> ><br>> ><br>> ><br>> >> multiple timesteps are not possible as far as gromacs 4.0.7. NAMD <br>> >> can do this.<br>> >><br>> >><br>> >> -- original message --<br>> >><br>> >> Is it possible to carry out multiple time step molecular<br>> >> dynamics simulations<br>> >> in Gromacs<br>> >> 4.0. versions ? Could you<br>> >> please give me some information about this issue ?<br>> >><br>> >> Thank you very much for your attention.<br>> >><br>> <br>> <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 />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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