Chris, I understand, Sorry for that . Actually I mixed up the concept of SteeredMd with umbrella sampling. So I was confused whenever you people gave suggestions.
Now I thing I got the idea , Thanks for you people. I will try myself and see. Thanks once again. -Aswathy On Tue, May 11, 2010 at 6:48 PM, <chris.ne...@utoronto.ca> wrote: > It represents a difference in coordinate space. You'll get the most out of > this list if you continue to try to solve your problems before posting and > avoid submitting every question/problem that you hit upon under a > continuously in-use title. Did you try it and look at you -px output file? I > suggest that you do some tutorials. Also, set up a test system and pull two > water molecules apart within a box of water and use VMD to see what happens. > Then try a slightly more difficult test system... these are the types of > things that worked for me. > > pull_init1 = 0 0 -5 > pull_init1 = 0 0 -4.9 > pull_init1 = 0 0 -4.8 > ... > pull_init1 = 0 0 4.9 > pull_init1 = 0 0 5 > > But it's up to you to determine the spacing. You need to get good overlap > in order to be able to do WHAM. If you don't know how to figure that out > then it's time for some reading. > > Good luck, > Chris. > > -- original message -- > > Hi Chris, > > Thank you very much for your detailed mail. > > Now I have a doubt on this pull_init parameter. i read your previous posts > regarding this, but still have a confusion. > > My query is that for each configuration when I run umbrella sampling, will > this pull_init value needs to change?(I suppose so, if its true how?) > > When it should be negative and positive? > > > Could you please explain this. Thanks for your valuable time > > Thanks & Regards, > Aswathy > > > On Mon, May 10, 2010 at 9:55 PM, Chris Neale <chris.ne...@utoronto.ca > >wrote: > > [Hide Quoted Text] > Pick a small collection of backbone atoms near the center of your channel > and use them as your reference group. Overcome the sign problem by optimal > selection of pull options (see below). pull_pbcatom values should not be > important > if you select your groups as I suggest -- otherwise be sure to understand > how they work. > > > ; COM PULLING > pull = umbrella > pull_geometry = position > pull_dim = N N Y > pull_start = no > pull_nstxout = 250 > pull_nstfout = 250 > pull_ngroups = 1 > pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS > pull_pbcatom0 = 0 > pull_group1 = LIGAND > pull_pbcatom1 = 0 > pull_init1 = 0 0 THISDIST > pull_rate1 = 0 > pull_k1 = 500.0 > pull_vec1 = 0 0 0 > > Chris. > > -- original message -- > > I think Justin meant that you have various positions of the ligand in the > channel (from the SMD), so you don't need to make a new run to determine > new > positions in the channel. You need only new umbrella sampling simulations. > > Yep, the movement of the particle will also matter, because if the particle > moves much on the z-axis, the distance between the particle and the ligand > will change. So you would want the particle fixed relative to the channel. > Two ideas: > Place the particle above the entrance of the channel. Pick three atoms from > the entrance of the channel and determine the distance between the atoms > and > the particle. Then use distance_restraints or constraints with a > 'bondlength' equal to the measured distance. If everything goes right the > particle would stay where you placed it, since it does not interact with > the > enviroment it should not really influence your simulation (only through the > constraints or distance_restraints). > I don't now how big your system is, but it would probably be a good idea to > make a short test simulation, to look if the particle changes the system > behavior. > But it's only an idea, i hope other people comment it. > > Greetings > Thomas > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy
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