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You really need pull_pbcatom0, since your slab is thicker than<br>half the box you otherwise can have periodicity errors.<br><br>Berk<br><br>> Date: Wed, 5 Aug 2009 15:27:06 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: pulling<br>> <br>> Hm..setting<br>> <br>> >>>> > >>> pull_geometry = direction<br>> >>>> > >>> pull_vec1 = 0 0 1<br>> >>>> <br>> should fix the pbc prob or do I need to set pull_pbcatom0 as well?<br>> Cause it still aint working using these settings (without the<br>> pull_pbcatom0).<br>> <br>> Thx,<br>> Alex<br>> <br>> Berk Hess schrieb:<br>> > 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<br>> > 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<br>> > 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<br>> > the pulling<br>> > > >>>> properly.<br>> > > >>>><br>> > > >>>> I have many configurations of a protein partially adsorbed to a<br>> > 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<br>> > 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<br>> > 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<br>> > of the<br>> > > >>>> protein completely onto the surface or very far away from it<br>> > depending<br>> > > >>>> on the value I use for pull_init1.<br>> > > >>>> So the distance between what and what shall I put for<br>> > 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>> > ------------------------------------------------------------------------<br>> > > >>> Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > >>> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><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<br>> > 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<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>> > > > _________________________________________________________________<br>> > > > Express yourself instantly with MSN Messenger! Download today it's<br>> > FREE!<br>> > > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> > > > -------------- next part --------------<br>> > > > An HTML attachment was scrubbed...<br>> > > > URL:<br>> > 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<br>> > 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<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>> > ------------------------------------------------------------------------<br>> > What can you do with the new Windows Live? Find out<br>> > <http://www.microsoft.com/windows/windowslive/default.aspx><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/' target='_new'>MSN Messenger</a></body>
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