[gmx-users] PMF of ligand transport

Aswathy ammasachu at gmail.com
Mon May 10 11:56:02 CEST 2010 

Thanks for your  reply.

 In this case reference (r57) is not the part of the channel. But it is a
residue in the loop above the channel entry. Thats why I used
pull_geometry=distance. Therefore I am pulling the ligand away from this
reference.

Thanks
-Aswathy

On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot <t.piggot at soton.ac.uk> wrote:

> Hi,
>
> If you defined the reference (r_57) as part of your channel then with
> pull_geometry=distance you will have problems as the distance between
> pull_group1 and pull_group0 becomes closer to zero and then the distance
> becomes positive again.
>
> I recently had this with my umbrella sampling simulations. Search for the
> discussion of things you can do to address this issue on the list. To stop
> this being a problem in the first place you should have used
> pull_geometry=position.
>
> Cheers
>
> Tom
>
> Aswathy wrote:
>
>> 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 <mailto:
>> 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
>>    <mailto: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
>>
>>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
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-- 
Aswathy
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