Re: [gmx-users] spurious forces while doing pulling simulation

[Justin A. Lemkul]

Amit Choubey wrote:
It seems that i cannot figure out a way to change the absolute reference 
point (Its the origin by default).


Nope.  You need to set an actual group of atoms as pull_group0 for a real 
reference, otherwise the reference point is always the origin.

-Justin

Amit

On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    Amit Choubey wrote:

        Yes Justin i understand that. Heres what i think is going on

        I dont have any reference group. Now the COM distance is
        calculated wrt the origin and whenever the COM is more than half
        of the box its causing problem.


    Correct.


        I think changing the absolute reference to the initial COM of
        the pull group (using pull_init1) should fix this issue but i am
        not confident.


    Using a defined reference group is the better method.  That way, the
    pull distance is calculated with respect to this reference, and it
    sounds like that will allow you to use the box you have already set up.

    -Justin

        Thanks for looking into this.

        On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



           Amit Choubey wrote:

               Hi,

               I am still not able to see the reason for the periodic
        distances
               coming into picture.


           I guess I don't fully understand your procedure.  If you only
        want
           to pull to a COM separation of 15 nm, there should be no problem,
           but yet you're achieving a COM separation of 18.5 nm?  That's
           exactly the problem.  If your box is 37 nm, 18.5 nm
        corresponds to
           the transition at which the code utilizes either the unit cell
           distance or the periodic distance as the restraint distance.
         So it
           is as this point that your forces go haywire.

           -Justin

               Also, why pull_geometry = direction_periodic cannot be
        used with
               P-coupling; although it seems to do what i want.

               Amit

               On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey
               <kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>
        <mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>>
               <mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>
        <mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>>>> wrote:

                  Hi,

                  Initially, the pull group center of mass is at 8.16 nm
        and i
               want to
                  pull 15 nm. I started with a box size of 37 nm in the pull
               direction.
                  The problem occurs when the COM is at 18.5 nm (ie at
        half the box
                  length).

                  Thanks for the attention.

                  Amit

                  On Mon, Jan 17, 2011 at 11:40 AM, 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:



                      Amit Choubey wrote:

                          Hi all,

                          I am trying to do pulling simulation.
        Following are
               the pull
                          parameters

                          pull = umbrella
                          pull_geometry = direction
                          pull_vec1 = 0 0 1
                          pull_group1 = RNA
                          pull_rate1 = 0.01
                          pull_k1 = 1000
                          pull_start = yes

                          Everything works fine until the pull group COM
               reaches half
                          the box length. The COM position changes by
        the box
               length
                          and that causes huge force on the group. What
        should
               i do to
                          fix this ? Also i am using NPT coupling.


                      You have to use a sufficiently large box,
        otherwise the
               periodic
                      distance becomes the reference distance when this
               happens.  This
                      has been discussed numerous times on the list (hint:
               there is an
                      archive for a reason!) and in the tutorial linked
        here:

                           
         http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

                      -Justin

                          Amit


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

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

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

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

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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