Thx for the quick reply! I use 4.0.5, pbc z=yes Box height = 17.5nm gld slab is from z=0 to z= 9.5; So distance=5.5 should give 1.0nm above surface right?
What do I have to put for pull_init1 if i use direction?? Thx, Alex Berk Hess schrieb: > Hi, > > I hope you are using 4.0.5, I fixed several bug in the pull code for > older 4.0 versions. > > The problems you are seing could be due to pbc. > Do you have pbc in Z, and what is the height of your box? > > A safer setup is: > pull_geometry = direction > pull_vec1 = 0 0 1 > But they should give the same answers if you do not have pbc issues. > > Berk > > > Date: Fri, 31 Jul 2009 12:13:07 +0200 > > From: alexander.h...@mytum.de > > To: gmx-users@gromacs.org > > Subject: [gmx-users] pulling > > > > Hey, > > > > I appear to have serious trouble understanding how to set up the pulling > > properly. > > > > I have many configurations of a protein partially adsorbed to a froozen > > surface (the configs differ > > in the amount of the protein that has been desorbed). > > Now I want the pulling to keep the distance of the desorbed end of the > > protein to the surface using the harmonic pot. > > Now the documentation is not very clear how this all works so I ran > > several experiments to figure it out but I failed. > > I use the following options: > > > > ;PULLING > > pull = umbrella > > pull_geometry = distance > > pull_dim = N N Y > > pull_nstxout = 1000 > > pull_nstfout = 1000 > > pull_ngroups = 1 > > pull_group0 = GLD > > pull_group1 = ASN > > pull_vec1 = 0.0 0.0 0.0 > > pull_init1 = 5.27778 > > pull_rate1 = 0.0 > > pull_k1 = 100 > > > > > > where gld is the surface and asn is the end residue of the protein and > > pull_init1 is set to the desired COM distance of the two > > groups (gld is froozen). I use the same settings for all runs, only > > changing pull_init1 to get the desired distance. > > Now for some reason using this setup either pulls the ASN end of the > > protein completely onto the surface or very far away from it depending > > on the value I use for pull_init1. > > So the distance between what and what shall I put for pull_init1? What > > else is wrong? > > > > Thx, > > Alex > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
