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No (completely) frozen groups are treated correctly.<br>I had to look in (my own) code again, but for a fully frozen group<br>the inverse mass is set to 0 in the pull code.<br><br>Berk<br><br>> Date: Fri, 31 Jul 2009 12:49:55 +0200<br>> From: schlesi@uni-mainz.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: pulling<br>> <br>> Could it also be possible that 'pull = distance' makes problems because<br>> it pulls both groups and here one group is frozen? Only an idea, i have<br>> never tried to pull a frozen molecule.<br>> Thomas<br>> <br>> <br>> > ------------------------------<br>> > <br>> > Message: 5<br>> > Date: Fri, 31 Jul 2009 12:38:19 +0200<br>> > From: Berk Hess <gmx3@hotmail.com><br>> > Subject: RE: [gmx-users] pulling<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <COL113-W5604F1D24936CF27D18DFE8E100@phx.gbl><br>> > Content-Type: text/plain; charset="iso-8859-1"<br>> > <br>> > <br>> > Ah, then you could have a pbc problem for determining the COM of the slab,<br>> > since you slab is thicker than half the box.<br>> > You have to set pull_pbcatom0 to an atom in the middle of the slab.<br>> > <br>> > pull_init1 doesn't change.<br>> > The only thing the geometry change affects is the direction you pull in.<br>> > With distance you could be unlucky that it takes the distance<br>> > in the opposite direction.<br>> > <br>> > Berk<br>> > <br>> >> Date: Fri, 31 Jul 2009 12:32:13 +0200<br>> >> From: alexander.herz@mytum.de<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: Re: [gmx-users] pulling<br>> >><br>> >> Thx for the quick reply!<br>> >><br>> >> I use 4.0.5, pbc z=yes<br>> >> Box height = 17.5nm<br>> >> gld slab is from z=0 to z= 9.5;<br>> >> So distance=5.5 should give 1.0nm above surface right?<br>> >><br>> >> What do I have to put for pull_init1 if i use direction??<br>> >><br>> >> Thx,<br>> >> Alex<br>> >><br>> >> Berk Hess schrieb:<br>> >>> Hi,<br>> >>><br>> >>> I hope you are using 4.0.5, I fixed several bug in the pull code for<br>> >>> older 4.0 versions.<br>> >>><br>> >>> The problems you are seing could be due to pbc.<br>> >>> Do you have pbc in Z, and what is the height of your box?<br>> >>><br>> >>> A safer setup is:<br>> >>> pull_geometry = direction<br>> >>> pull_vec1 = 0 0 1<br>> >>> But they should give the same answers if you do not have pbc issues.<br>> >>><br>> >>> Berk<br>> >>><br>> >>>> Date: Fri, 31 Jul 2009 12:13:07 +0200<br>> >>>> From: alexander.herz@mytum.de<br>> >>>> To: gmx-users@gromacs.org<br>> >>>> Subject: [gmx-users] pulling<br>> >>>><br>> >>>> Hey,<br>> >>>><br>> >>>> I appear to have serious trouble understanding how to set up the pulling<br>> >>>> properly.<br>> >>>><br>> >>>> I have many configurations of a protein partially adsorbed to a froozen<br>> >>>> surface (the configs differ<br>> >>>> in the amount of the protein that has been desorbed).<br>> >>>> Now I want the pulling to keep the distance of the desorbed end of the<br>> >>>> protein to the surface using the harmonic pot.<br>> >>>> Now the documentation is not very clear how this all works so I ran<br>> >>>> several experiments to figure it out but I failed.<br>> >>>> I use the following options:<br>> >>>><br>> >>>> ;PULLING<br>> >>>> pull = umbrella<br>> >>>> pull_geometry = distance<br>> >>>> pull_dim = N N Y<br>> >>>> pull_nstxout = 1000<br>> >>>> pull_nstfout = 1000<br>> >>>> pull_ngroups = 1<br>> >>>> pull_group0 = GLD<br>> >>>> pull_group1 = ASN<br>> >>>> pull_vec1 = 0.0 0.0 0.0<br>> >>>> pull_init1 = 5.27778<br>> >>>> pull_rate1 = 0.0<br>> >>>> pull_k1 = 100<br>> >>>><br>> >>>><br>> >>>> where gld is the surface and asn is the end residue of the protein and<br>> >>>> pull_init1 is set to the desired COM distance of the two<br>> >>>> groups (gld is froozen). I use the same settings for all runs, only<br>> >>>> changing pull_init1 to get the desired distance.<br>> >>>> Now for some reason using this setup either pulls the ASN end of the<br>> >>>> protein completely onto the surface or very far away from it depending<br>> >>>> on the value I use for pull_init1.<br>> >>>> So the distance between what and what shall I put for pull_init1? What<br>> >>>> else is wrong?<br>> >>>><br>> >>>> Thx,<br>> >>>> Alex<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<br>> >>> 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>> >>> Express yourself instantly with MSN Messenger! MSN Messenger<br>> >>> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><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>> >> 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>> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> > -------------- next part --------------<br>> > An HTML attachment was scrubbed...<br>> > URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090731/22c5d4e2/attachment.html<br>> > <br>> > ------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list<br>> > 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>> > <br>> > End of gmx-users Digest, Vol 63, Issue 161<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 />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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