[gmx-users] PMF of ligand transport
ammasachu at gmail.com
Mon May 17 08:44:59 CEST 2010
I tried to calculate PMF for the ligand transport using
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
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
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.
On Tue, May 11, 2010 at 11:15 AM, Aswathy <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,
> On Mon, May 10, 2010 at 9:55 PM, Chris Neale <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
>> 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
>> -- 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
>> 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
>> But it's only an idea, i hope other people comment it.
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