[gmx-users] PMF of ligand transport

[Aswathy]

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 <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>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
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