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Ah, now I see what the problem is.<br>The pull code works correctly when the distance is shorter or longer<br>than half the box length. But when the distance crosses half the box length,<br>the code might take the "wrong" periodic distance.<br>I'll see if I can fix this.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] t_trxframe speed units<br>Date: Fri, 4 Sep 2009 10:25:09 +0200<br><br>
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Hi,<br><br>Could you mail me your input files?<br><br>Berk<br><br>> Date: Fri, 4 Sep 2009 10:05:27 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] t_trxframe speed units<br>> <br>> Hi<br>> <br>> yes, I tried pull_start=yes (you also suggested trying constraint<br>> instead of umbrella, which I tried as well).<br>> my box is rectangular.<br>> <br>> Alex<br>> <br>> Berk Hess schrieb:<br>> > Hi,<br>> ><br>> > The only thing I suggested was using pull_start=yes,<br>> > otherwise you will start at a "random" distance and you will have enormous forces.<br>> > Did you try that?<br>> ><br>> > Do you have a rectangular or a triclinic box?<br>> ><br>> > Berk<br>> ><br>> > <br>> >> Date: Thu, 3 Sep 2009 18:00:44 +0200<br>> >> From: alexander.herz@mytum.de<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: Re: [gmx-users] t_trxframe speed units<br>> >><br>> >> Hey,<br>> >><br>> >> I tried everything you suggested and a couple more things and still it<br>> >> is not possible to get a reasonable speed<br>> >> for the pulled groups (always way beyond the 0.01nm/ps set in the mdp<br>> >> file and mostly containing some high frequence patttern probably related<br>> >> to pbc). (I tried: constraint, pbcatoms, direction,position and using no<br>> >> ref group).<br>> >><br>> >> Can I send you a small sample system with the problem or is there<br>> >> something else I can do?<br>> >><br>> >> Thx,<br>> >> Alex<br>> >><br>> >> Berk Hess schrieb:<br>> >> <br>> >>> But you can not talk about popping back, since there is pbc.<br>> >>> What matters is how the pull code determines the distance.<br>> >>> At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc,<br>> >>> such that it pulls smoothly even if the distance is larger than the box<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>> _______________________________________________<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/">MSN Messenger</a><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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