Re: [gmx-users] PMF of ligand transport

[Justin A. Lemkul]

Aswathy wrote:

Thank you very much for all replies.

No w I just want to try SMd with geometry type as position . But one 
thing is still confusing me, ie; reference group.


If you have already generated a suitable set of positions from which you have 
generated umbrella sampling windows, you do not need to repeat the SMD.  Your 
problem was only related to the actual umbrella sampling itself.

 I have the ligand in the solvent (at the mouth of the 
channel(extracellular).) Now I want to pull this ligand to the 
intracellular solvent through the channel. My understanding is that the 
reference group should be the in the same direction of the channel(ie, 
at the intracellular end of the channel), so that if I use "position", 
the ligand should move towards the reference group (Please correct me if 
this wrong). i have only solvent at this end(end of the channel) . Can I 
set water molecules as reference point? or any molecule at this 
intracellular end is fine?


In theory, you can set whatever you want, but if those water molecules diffuse, 
then you're trying to hit a rapidly-moving target!  Always choose a relatively 
static part of the structure in the direction you want to pull.

-Justin

Or else my understanding is wrong?

Please help me

Thank you.

Aswathy


On Mon, May 10, 2010 at 6:50 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    Aswathy wrote:



        On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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)?


    A residue with a more predictable position is probably preferable.
     If the loop moves a lot (or even somewhat), the umbrella potential
    will attempt to maintain the specified reference distance, so you
    could get spurious forces.

    -Justin

           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
               <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:



                  Aswathy wrote:

                      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.


                  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.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk> <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk>>
               <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk> <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk>>>
                      <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk>
               <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk>> <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@soton.ac.uk>
               <mailto:t.pig...@soton.ac.uk
        <mailto:t.pig...@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
                      <ammasa...@gmail.com <mailto:ammasa...@gmail.com>
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                      <mailto:ammasa...@gmail.com
        <mailto:ammasa...@gmail.com> <mailto:ammasa...@gmail.com
        <mailto:ammasa...@gmail.com>>
               <mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>
        <mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>>>

                             <mailto:ammasa...@gmail.com
        <mailto:ammasa...@gmail.com>
               <mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>>
                      <mailto:ammasa...@gmail.com
        <mailto:ammasa...@gmail.com>
               <mailto:ammasa...@gmail.com
        <mailto:ammasa...@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
                             <joc...@xray.bmc.uu.se
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               <mailto:joc...@xray.bmc.uu.se
        <mailto:joc...@xray.bmc.uu.se>>>>
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               <mailto:joc...@xray.bmc.uu.se <mailto:joc...@xray.bmc.uu.se>>
                      <mailto:joc...@xray.bmc.uu.se
        <mailto:joc...@xray.bmc.uu.se> <mailto:joc...@xray.bmc.uu.se
        <mailto:joc...@xray.bmc.uu.se>>>
                             <mailto:joc...@xray.bmc.uu.se
        <mailto:joc...@xray.bmc.uu.se>
               <mailto:joc...@xray.bmc.uu.se <mailto:joc...@xray.bmc.uu.se>>
                      <mailto:joc...@xray.bmc.uu.se
        <mailto:joc...@xray.bmc.uu.se>
               <mailto:joc...@xray.bmc.uu.se
        <mailto:joc...@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


                  --     ========================================

                  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> <http://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 <http://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 <http://vt.edu> | (540) 231-9080
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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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