[gmx-users] PMF of ligand transport

[Aswathy]

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.neale at 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.neale at 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
>
>
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-- 
Aswathy
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