[gmx-users] PMF of ligand transport

[Aswathy]

Can any one help me please? I looking forward to hear from any of you.
Thank you.


On Thu, May 6, 2010 at 1:19 PM, Aswathy <ammasachu at gmail.com> wrote:

> Ok i will explain you in detail.
>
>  Initially i pulled the ligand through the protein channel , using the
> given parameters.
>
> pull                     = umbrella
> pull_geometry            = distance
> pull_dim                 =  N N Y
> pull_start               = yes
> pull_nstxout             =  10
> pull_nstfout             =  10
> pull_ngroups             =  1
> pull_group0              =  r_57
> pull_group1              =  r_C1
> pull_rate1               =  0.01
> pull_k1                  =  1500
>
> Then I extracted the frames from the trajectory using the perl program
> provided with tutorial. COM distance I took as nearly 0.12 nm. (But
> sometimes I failed to obtain frames exactly at that interval, but took
> nearly at 0.12). Each frame I used for Umbrella sampling for 1ns.
> Then I checked histograms for overlapping (Some histograms were entirely
> overlapped and I removed that from the list, where ever gaps i selected new
> frames and did sampling so that I can get an evenly distributed histograms ,
> I know this will change the overall COM distribution but is there any other
> way to solve this?) .
>
> Finally once I obtained reasonably good overlapped histograms, I plotted
> PMF using g_wham. The plot  was a steeply increasing potential.  How can we
> get increased PMF even when the ligand is reached out of the channel?
>



> Did I made any mistake any where , I am confused.
>
> Thank you.
> -Aswathy
>
>
>
> On Thu, May 6, 2010 at 12:56 PM, Jochen Hub <jochen at xray.bmc.uu.se> wrote:
>
>> Aswathy wrote:
>>
>>>
>>> Hi gromacs users,
>>>
>>> I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport
>>> through a channel.
>>>
>>> I performed SMD and did umbrella sampling (Thanks to Justin for his
>>>  tutorial). Extracted frames with a window spacing interval  of ~0.12nm. and
>>> did 1ns sampling. Histograms are with reasonabvle overlap. Then I used
>>> g_wham for plotting PMF considering first 300ps as equilibration.
>>>
>> Isn't SMD usually referred to pulling at some finite pulling speed? That
>> would not be umbrella sampling.
>>
>> Anyway, you'll have to provide a lot more data to enable us to help you.
>>
>> Jochen
>>
>>
>>
>>
>>> I am getting a plot , but potential is increasing constantly. ie, PMF is
>>> not converged as mentioned the tutorial? Do I need to extend the sampling ?
>>> or any other reason?
>>>
>>> Please help me.
>>> Thank you.
>>>
>>> -Aswathy
>>>
>>
>>
>> --
>> ---------------------------------------------------
>> Dr. Jochen Hub
>> Molecular Biophysics group
>> Dept. of Cell & Molecular Biology
>> Uppsala University. Box 596, 75124 Uppsala, Sweden.
>> Phone: +46-18-4714451 Fax: +46-18-511755
>> ---------------------------------------------------
>>
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>
>
>
> --
> Aswathy
>



-- 
Aswathy
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