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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>> > ------------------------------------------------------------------------<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>> _______________________________________________<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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