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? Read http://www.gromacs.org/mailing_lists/users.php >>> ------------------------------------------------------------------------ >>> Express yourself instantly with MSN Messenger! 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