[gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

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.

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.

Thanks for looking into this.

On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul <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>> 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
>
> ========================================
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