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Hi,<br><br>Are you running in parallel with domain decomposition?<br>In that case it will probably not work, I forgot to add a check<br>for angular comm removal with domain decomposition.<br><br>It should work single cpu and with particle decomposition (mdrun -pd).<br><br>Berk<br><br>> From: p.woiczikowski@tu-bs.de<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 11 Dec 2008 15:35:22 +0100<br>> Subject: [gmx-users] Re: DNA will not stay in the middle of the box (Nicolas)<br>> <br>> Hi again,<br>> <br>> I am aware that it is not quite physical to do so, but in this particular <br>> project it really helps to use such a protocol.<br>> <br>> Indeed, it worked perfectly in 3.3, so why should that not work with 4.0? May <br>> there be a bug in 4.0?<br>> <br>> Regards,<br>> Ben<br>> <br>> >I think this question has been already addressed for proteins. Anyway, <br>> >removing the COM motions of only one component of your system is very <br>> >probably a bad idea. You should rather use position restraints. If you <br>> >look in the mailing-list or the manual, you will quickly find how to do <br>> >that.<br>> ><br>> >Regards,<br>> >Nicolas<br>> <br>> <br>> >> Hi,<br>> >><br>> >> I simulate DNA molecules in water with counterions. To keep the DNA in the <br>> >> middle of the box I had the following options in the input file:<br>> >><br>> >> comm_mode = angular<br>> >> comm_grps=dna<br>> >> <br>> > > For the old version (3.3.2) it worked but now (4.0.2) there are warnings <br>> and <br>> >> at the end the DNA doens't stay in the middle of the box.<br>> >><br>> >> Can somebody help?<br>> >><br>> >> Regards,<br>> >> Ben<br>> >> <br>> -- <br>> <br>> <br>> -------------------------------------------------------------------------<br>> Paul Benjamin Woiczikowski<br>> Department of Physical and Theoretical Chemistry<br>> Technische Universität Braunschweig<br>> Hans-Sommer Strasse 10<br>> D-38106 Braunschweig<br>> Germany<br>> <br>> Phone: <br>> Office +49(0)531 3915348<br>> Home +49(0)531 4737646<br>> Mobile +49(0)176 63168158<br>> <br>> Mail:<br>> p.woiczikowski@tu-bs.de<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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