[gmx-users] spurious forces while doing pulling simulation
Justin A. Lemkul
jalemkul at vt.edu
Tue Jan 18 12:31:55 CET 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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.amit at gmail.com <mailto:kgp.amit at gmail.com>
> <mailto:kgp.amit at gmail.com <mailto:kgp.amit at gmail.com>>
> <mailto:kgp.amit at gmail.com <mailto:kgp.amit at gmail.com>
> <mailto:kgp.amit at gmail.com <mailto:kgp.amit at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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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