[gmx-users] PMF of ligand transport

Aswathy ammasachu at gmail.com
Mon May 17 12:05:48 CEST 2010 

On Mon, May 17, 2010 at 12:14 PM, Aswathy <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?



> 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
>



-- 
Aswathy
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