# [gmx-users] PMF of ligand transport

Aswathy ammasachu at gmail.com
Mon May 10 15:18:57 CEST 2010

```On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Ok . Now I understood. I have one more doubt , as I mentioned to you, I am
> using one residue in the extracellular loop as a reference point. Since this
> is in the loop, do you think it can be good reference point (due to th large
> fluctuatuion in the loop, will it affect the result)?
>
> Aswathy wrote:
>
>> I am pulling through the channel with respect to a single residue on one
>> "side"(extracellular) of the structure. I have used pull_geometry = distance
>> &  pull_dim =  N N Y. From this what I understood is ligand will pull along
>> the z direction with respect to the reference group (away from r_57).  (i.e
>> from extracellular to intracellular). Is this correct?
>>
>>
> I don't think so.  If you are pulling through a channel, using an
> extracellular residue as a reference, you will be changing the sign of the
> distance, rendering "pull_geometry = distance" useless.  For example, in
> order to properly calculate the PMF, you have to pull from the aqueous
> solvent, into the channel, then back out into the solvent.  At some point,
> your ligand is outside the channel (such that, for example, the z-coordinate
> of the ligand is greater than that of r_57, so distance > 0).  Then, as your
> ligand enters the channel, its z-coordinate is less than that of r_57, so
> distance < 0.  If this is the case, you must use "pull_geometry = position"
> to get the correct signs, otherwise your umbrella sampling window reference
> distances will be nonsensical.
>
> -Justin
>
>  Here is my umbrella sampling .mdp 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_k1                  =  1000
>> pull_init1               =  0
>>
>> On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Aswathy wrote:
>>
>>
>>         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.
>>
>>
>>    So you are not pulling through the channel?  Or you are pulling
>>    through the channel with respect to a single residue on one "side"
>>    of the structure?  If your ligand ever crosses over this reference
>>    in any way, the reference distance will change sign and thus Tom is
>>    right, you should use "pull_geometry = position."  With "distance,"
>>    you can only ever have positive reference distances.
>>
>>    What are your .mdp settings during umbrella sampling?
>>
>>    -Justin
>>
>>        Thanks
>>        -Aswathy
>>
>>
>>        On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot
>>        <t.piggot at soton.ac.uk <mailto:t.piggot at soton.ac.uk>
>>        <mailto:t.piggot at soton.ac.uk <mailto: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>
>>               <mailto:ammasachu at gmail.com <mailto:ammasachu at gmail.com>>
>>        <mailto:ammasachu at gmail.com <mailto:ammasachu at gmail.com>
>>
>>               <mailto: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>
>>        <mailto:jochen at xray.bmc.uu.se <mailto:jochen at xray.bmc.uu.se>>
>>                  <mailto:jochen at xray.bmc.uu.se
>>        <mailto:jochen at xray.bmc.uu.se>
>>               <mailto: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
>>
>>                      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?
>>
>>                          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
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>
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>>
>>
>>
>> --
>> Aswathy
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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