[gmx-users] spurious forces while doing pulling simulation

[Justin A. Lemkul]

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>> 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>> 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> | (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

========================================