[gmx-users] PMF of ligand transport
Justin A. Lemkul
jalemkul at vt.edu
Mon May 17 13:08:46 CEST 2010
Aswathy wrote:
>
>
> On Mon, May 17, 2010 at 12:14 PM, Aswathy <ammasachu at gmail.com
> <mailto:ammasachu at gmail.com>> wrote:
>
> 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 = 0
> 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?
>
>
> I want to add some more points to this. I agree that as I am using the
> "Position" , it should be displaced to the position of reference. But my
> worry is that, when i visualize this trajectory, within the first two or
> three frames, ligand get displaced. As per my u understanding, we need
> to sample well at the same position to get the PMF at that point.(Is it
> so?) in that case, the sudden drop from the initial position will cause
> any problem in the PMF?
>
There is nothing wrong. Your ligand will move around; that's what MD does. As
long as the reference distance between your ligand and bilayer remains correct
there is no problem. The umbrella potential is a harmonic restraining force,
allowing for some deviation in position such that the ligand about the sampling
window. If there is some drastic change in position such that this reference
distance is no longer conserved, then you have a problem. But certainly this is
not what is happening within only a few frames.
-Justin
>
>
> Is there anything wrong that I am doing?
> any suggestions will be appreciated.
>
> -Aswathy
>
>
>
> On Tue, May 11, 2010 at 11:15 AM, Aswathy <ammasachu at gmail.com
> <mailto:ammasachu at 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.neale at utoronto.ca <mailto:chris.neale at 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
>
>
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>
>
>
> --
> Aswathy
>
>
>
>
> --
> Aswathy
>
>
>
>
> --
> Aswathy
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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