Hm..setting >>>> > >>> pull_geometry = direction >>>> > >>> pull_vec1 = 0 0 1 >>>> should fix the pbc prob or do I need to set pull_pbcatom0 as well? Cause it still aint working using these settings (without the pull_pbcatom0).
Thx, Alex Berk Hess schrieb: > No (completely) frozen groups are treated correctly. > I had to look in (my own) code again, but for a fully frozen group > the inverse mass is set to 0 in the pull code. > > Berk > > > Date: Fri, 31 Jul 2009 12:49:55 +0200 > > From: [email protected] > > To: [email protected] > > Subject: [gmx-users] Re: pulling > > > > Could it also be possible that 'pull = distance' makes problems because > > it pulls both groups and here one group is frozen? Only an idea, i have > > never tried to pull a frozen molecule. > > Thomas > > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Fri, 31 Jul 2009 12:38:19 +0200 > > > From: Berk Hess <[email protected]> > > > Subject: RE: [gmx-users] pulling > > > To: Discussion list for GROMACS users <[email protected]> > > > Message-ID: <[email protected]> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > Ah, then you could have a pbc problem for determining the COM of > the slab, > > > since you slab is thicker than half the box. > > > You have to set pull_pbcatom0 to an atom in the middle of the slab. > > > > > > pull_init1 doesn't change. > > > The only thing the geometry change affects is the direction you > pull in. > > > With distance you could be unlucky that it takes the distance > > > in the opposite direction. > > > > > > Berk > > > > > >> Date: Fri, 31 Jul 2009 12:32:13 +0200 > > >> From: [email protected] > > >> To: [email protected] > > >> Subject: Re: [gmx-users] pulling > > >> > > >> 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: [email protected] > > >>>> To: [email protected] > > >>>> 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 [email protected] > > >>>> 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 [email protected]. > > >>>> Can't post? 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Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
