Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position.
Let me explain you what I did so far, I picked a small collection of backbone atoms nearly from the centre of the channel.My SMD was displacing the ligand from extracellular to intracellular. I checked the pullx file for getting the window spacing (pull_init ). Initial structure is at =7.61 Centre of the channel(reference) =8.20 Last displacement is at =8.91 Therfore I selected pul_init as 0.6, 0.5, 0.4 ,....0....-0.4,-0.5,-0.6 For example, the first frame(at 7.61) was sampled using the following parameters, pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0 = 0 pull_group1 = r_C1 pull_pbcatom1 = 0pull_k1 = pull_init1 = 0 0 0.6 pull_k1 = 1000 pull_rate1 = 0 pull_vec1 = 0 0 0 The problem is that the ligand undergoes a displacement to wrong direction during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in one place where it get sampled? Is there anything wrong that I am doing? any suggestions will be appreciated. -Aswathy On Tue, May 11, 2010 at 11:15 AM, Aswathy <ammasa...@gmail.com> wrote: > 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: > >> 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 the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Aswathy > -- Aswathy
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