Re: [gmx-users] Umbrella Pulling

Justin A. Lemkul Fri, 17 Feb 2012 06:53:52 -0800


Steven Neumann wrote:

On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:




    Steven Neumann wrote:

        Hello Justin,

        As you recommended I run longer pulling of my ligand. I pull the
        ligand which is on the top of my protein so the top of the
        protein is pulled so that the whole protein rotated app. 30
        degrees - the low part of the protein came out of the box due to
        the rotation. After app 600 ps the ligand does not move any more
        and the force applied increase linearly. As I saw the
        trajectory, ligand does not collide with a periodic image but it
        does not move. Please, see attacheg plot force vs time. Can you
        explain why the force increase linearly and ligand is not pulled
        any more? This is my mdp file for pulling:


    Is the pulled distance greater than half of the box vector in z?
     That's the only reason I can see things going haywire.  With simple
    "distance" geometry, there are some limitations like that.  Rotation
    itself is not a problem.  You're separating two objects; there's no
    clear orientation dependence in that case.

    -Justin

As you can see the pulling distance is 5 nm. The lenght of my box in Zdirection is 12 nm. Thus, it is not. Any other ideas?

No, it's not. You're doing 1 ns of simulation (contrary to the comment, 500000* 0.002 = 1000 ps) and thus pulling at 10 nm per ns you are trying to pull 10 nmin this simulation. So once your molecule hits 6 nm (right at about 600 ps fromyour plot and the expected pull rate), you're violating the criterion that Isuspected.


-Justin


        title       = Umbrella pulling simulation
        ; Run parameters
        integrator  = md
        dt          = 0.002
        tinit       = 0
        nsteps      = 500000    ; 500 ps
        nstcomm     = 10
        ; Output parameters
        nstxout     = 5000      ; every 10 ps
        nstvout     = 5000
        nstfout     = 500
        nstxtcout   = 500       ; every 1 ps
        nstenergy   = 500
        ; Bond parameters
        constraint_algorithm    = lincs
        constraints             = all-bonds
        continuation            = yes       ; continuing from NPT
        ; Single-range cutoff scheme
        nstlist     = 5
        ns_type     = grid
        rlist       = 0.9
        rcoulomb    = 0.9
        rvdw        = 0.9
        ; PME electrostatics parameters
        coulombtype     = PME
        fourierspacing  = 0.12
        fourier_nx      = 0
        fourier_ny      = 0
        fourier_nz      = 0
        pme_order       = 4
        ewald_rtol      = 1e-5
        optimize_fft    = yes
        ; Temperature coupling is on
        tcoupl      = V-rescale                     ; modified Berendsen
        thermostat
        tc_grps     = Protein_LIG Water_and_ions   ; two coupling groups
        - more accurate
        tau_t       = 0.1   0.1                     ; time constant, in ps
        ref_t       = 298   298                     ; reference
        temperature, one for each group, in K
        ; Pressure coupling is on
        Pcoupl          = Parrinello-Rahman
        pcoupltype      = isotropic
        tau_p           = 1.0      compressibility = 4.5e-5
        ref_p           = 1.0
        ; Generate velocities is off
        gen_vel     = no
        ; Periodic boundary conditions are on in all directions
        pbc     = xyz
        ; Long-range dispersion correction
        DispCorr    = EnerPres
        ; Pull code
        pull            = umbrella
        pull_geometry   = distance  ; simple distance increase
        pull_dim        = N N Y
        pull_start      = yes       ; define initial COM distance > 0
        pull_ngroups    = 1
        pull_group0     = Protein
        pull_group1     = LIG182
        pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
        pull_k1         = 200      ; kJ mol^-1 nm^-2

        Would you recommend position restrained of the protein backbone
        atoms or e.g. residues from the lower part so that the protien
        will not roatate?

        Thank you,

        Steven







           On Fri, Feb 17, 2012 at 10:41 AM, Steven Neumann
           <s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>
        <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>__>
        wrote:





               On Mon, Feb 13, 2012 at 2:53 PM, Steven Neumann
               <s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>
        <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>__>
        wrote:

                   Thank you Justin!


                   On Mon, Feb 13, 2012 at 2:44 PM, Justin A. Lemkul
                   <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



                       Steven Neumann wrote:

                           Thank you Justin. I run my pulling using two
        force
                           constant for pulling. K1=100 and K1=200
                           Please, see attached plots of force vs time. Is
                           there any criteria to adjust pulling
        constant? Would
                           you suggest running it for a longer time?


                       I know of no systematic study for choosing a force
                       constant.  Guessing wildly at what's going on,
        I'd say
                       you need longer simulations as it appears you
        have only
                       just caused dissociation towards the end of the
        500 ps.

                       -Justin

                           Steven

                           On Mon, Feb 13, 2012 at 1:11 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:



                              Steven Neumann wrote:

                                  Dear Gmx Users,
                                   Is it always required to restrained
                           positions of the protein
                                  while pulling your ligand? My system
        is made
                           of 10 ligands
                                  attached to my protein surface. I am
        pulling
                           one of them.


                              No, it is not required.  I assume you've
        gotten
                           this idea from my
                              tutorial - the restraints there were used
        for a
                           very specific
                              purpose (detailed in the paper linked from the
                           tutorial).


                                  I have just seen trajectory of pulling my
                           ligand without
                                  restraining positions of protein and 9
                           remaining ligands. My
                                  ligand while pulling also pulled the
        protein
                           with itself (for 1
                                  nm distance) and then splited. Is is this
                           approach more reliable?

If your goal is umbrella sampling, you

        need only
                           generate a series
                              of reasonable starting configurations along a
                           defined reaction
                              coordinate.  The absolute positions are
                           irrelevant; it is the
                              relative distance that matters.

                              -Justin

--==============================______==========




                              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
        <tel:%28540%29%20231-9080>
                           <tel:%28540%29%20231-9080>
                              <tel:%28540%29%20231-9080>
                              http://www.bevanlab.biochem.

<http://www.bevanlab.biochem./__>____vt.edu/Pages/Personal/__justin

        <http://vt.edu/Pages/Personal/justin>
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------------------------------____----------------------------__--__------------

--==============================____==========


                       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 <tel:%28540%29%20231-9080>
                       <tel:%28540%29%20231-9080>

http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin

        <http://vt.edu/Pages/Personal/justin>

<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin

        <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>

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------------------------------__------------------------------__------------

--==============================__==========


    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
    <tel:%28540%29%20231-9080>
    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>

    ==============================__==========

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

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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Re: [gmx-users] Umbrella Pulling

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