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Hi,<br><br>I hope you are using 4.0.5, I fixed several bug in the pull code for 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 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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