[gmx-users] spurious forces while doing pulling simulation
Amit Choubey
kgp.amit at gmail.com
Tue Jan 18 04:28:14 CET 2011
It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).
Amit
On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul <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>> 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>>> 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>>> 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> |
>>
>> (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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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