# [gmx-users] Rupture force definition

Rakesh Mishra rockinbhu at gmail.com
Thu May 10 07:24:33 CEST 2018

```Dear Justin,

I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs
But  I faced two more basic problem in gromacs.

1-   I need double size box if I need to pull half distance of box (Which
makes time demanding ).
Eg.  let I want to pull DNA of length 34 Angstroms (3.4 nm) to 68
Angstroms (6.8 nm) along X direction.
Then I need to make the box of the  size just double of 6.8 nm i.e
we need to box that must be extended in the pulling direction of the size
13. 6 nm.
And then it needs lots of time to simulate compare to if I use other
simulation tool for  pulling like NAMD or Amber, where no need to make the
box size double
then the given pulling distance. Then  Why Gromacs should be used for
pulling .

2-  And I use constant velocity pulling with distance increasing. Then Its
not possible to get variation of force/distance . It just gives linear
variation like straight line with force.
Yes, it gives basically variation of force with the time .

3-  But suppose we want get force versus stretch(extension) curve then how
to do constant force pulling like constant velocity.

4-  Should we use NAMD for simple force versus extension curve .

My above 1-2-3 questions are important for me as a gromacs user.  If
possible please ans, I will be great full to you.

On Fri, Feb 16, 2018 at 12:40 PM, Rakesh Mishra <rockinbhu at gmail.com> wrote:

> Dear Justin thanks for detail.
>
> Initially my system was positioned along the x direction. final structure,
> that we got After 10 ns generation for pulling
> that system is slightly tilts toward the z direction but not exactly.
> Please find the attache snapshot of tilted picture.
> In this picture, I am trying to pull the left side end (in the downward z
> direction),which is close to the z axis.
>
>
>
> On Thu, Feb 15, 2018 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/15/18 4:13 AM, Rakesh Mishra wrote:
>>
>>>
>>> I will check for longer run for getting response according to you.
>>>
>>>
>>> I would like to explain my system,which is siRNA of chain A and B.
>>> Here, after doing all formalities, I had run 10 ns then try to apply the
>>> pull protocol.
>>>
>>> See, here for pulling this system, I have restricted 1st residue of
>>> chain-A, and pulling last ( 22th)
>>> residue of chain-B, which is at the same side end just below the 1st
>>> residue of chain-A.
>>> ( means, both reference and pull groups are at the same end side ).
>>>
>>> Note- I am pulling this 22th residue of chain-B in the downward (-z)
>>> direction with negative rate.
>>>           ( here pull group is below from the reference group)
>>>
>>> I also  followed your advise to pull with negative rate with high spring
>>> constant. But  in this case also,
>>> system is not moving in the downwards (-z  ) direction.
>>>
>>> Interesting-
>>> But the most interesting case is that for the same system just discussed
>>> above, when I am
>>> applying pulling code with + rate even with smaller spring constant, then
>>> system is moving in
>>> downward (-z) direction. While In my thinking, because I have given
>>> +rate,
>>> so it should move in
>>> the + z direction. So, could it be possible that there is one thing that
>>> can also matter ,
>>> i.e. whether, pull group is below and reference group is above .
>>>
>>> Because in the same system, when I pull 22the residue of chain-A w.r.t
>>> reference residue 1 of chain-B
>>> (which is slightly below from the pull residue 22th of chain-A) with the
>>> same +rate and spring constant.
>>> In this case pull group moves in the + z direction (upward), which I
>>> expect
>>> ( note-  here pull group is
>>> slightly above from the reference group)
>>>
>>> So, this contradiction with effect based on the end side pulling and
>>> posing
>>> of reference and pull groups
>>> is making it surprise and trouble.
>>>
>>
>> How is the RNA oriented? Is the z-axis coincident with the helical axis?
>> If so, that's a poor choice for a reaction coordinate and you should choose
>> a different axis, orthogonal to the helix. Or just pull in all dimensions
>> so that it's the total COM distance between the base pair. Remember, the
>> tutorial is a special case in which a one-dimension pull made sense due to
>> the inherent geometry of the unidirectional growth model of amyloid
>> fibrils. Do not assume that all system should be treated this way.
>>
>> The negative pull rate means "bring the two specified groups together"
>> not necessarily "pull along -z" so be sure your orientation convention
>> aligns with what you're trying to do.
>>
>> -Justin
>>
>>
>>>
>>>
>>>
>>> On Wed, Feb 14, 2018 at 7:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 2/14/18 7:31 AM, Rakesh Mishra wrote:
>>>>
>>>> Dear Justin,
>>>>>
>>>>> Can you explain something regarding this issue.
>>>>>
>>>>> I couldn't get  resolve one  problem.  Though now I am able to make
>>>>> restrict (immobile )
>>>>> the needed residue and pulled another one.
>>>>> But the contradiction that i am facing is that, when I am pulling with
>>>>> -rate (in negative z direction, as I want to pull
>>>>> the residue in the negative Z direction of box ) given below.
>>>>> Still there we see  that pulling group is not moving the -ve direction
>>>>> of
>>>>> z.
>>>>>
>>>>> Your settings are right, so either you need a larger force constant to
>>>> induce the motion or you need to wait longer for the restoring forces in
>>>> the system (whatever they are) to be overcome by the biasing potential.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> pull                           = yes
>>>>> pull_ngroups              = 2
>>>>> pull_ncoords              = 1
>>>>> pull_group1_name          = chain-A-start
>>>>> pull_group2_name          = chain-B-end
>>>>> pull_coord1_type            = umbrella      ; harmonic biasing force
>>>>> pull_coord1_geometry    = distance      ; simple distance increase
>>>>> pull_coord1_groups         = 1 2
>>>>> pull_coord1_dim             = N N Y
>>>>> pull_coord1_rate            = -0.01          ;  0.01 nm per ps = 10
>>>>> per 1
>>>>> ns
>>>>> pull_coord1_k                = 1000          ; kJ mol^-1 nm^-2
>>>>> pull_coord1_start           = yes           ; define initial COM
>>>>> distance
>>>>> 0
>>>>>
>>>>>
>>>>> Best
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra <rockinbhu at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Thank you very much Justin.
>>>>>
>>>>>> Here it is working but having some  problem.
>>>>>> pull_group2_name = chain_B35  is moving in the + z direction &
>>>>>> pull_group4_name= chain_B26   is  moving oppositely in the -z
>>>>>> direction
>>>>>> While I have given pull in +z direction for both the above group.
>>>>>>
>>>>>> Note - pull_group1_name = chain_A8 and  pull_group3_name  = chain_A17
>>>>>> are
>>>>>> immobile here as well as acting as reference.
>>>>>>
>>>>>>
>>>>>> On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> On 2/1/18 7:59 AM, Rakesh Mishra wrote:
>>>>>>>
>>>>>>> Dear Justin
>>>>>>>
>>>>>>>> Here I am applying pull for two groups with respect to two reference
>>>>>>>> group
>>>>>>>> as following.
>>>>>>>> ; Pull code
>>>>>>>> pull                    = yes
>>>>>>>> pull_ngroups            = 4
>>>>>>>> pull_ncoords            = 1
>>>>>>>> pull_group1_name        = chain_A8     (reference  also immobile )
>>>>>>>> pull_group2_name        = chain_B35   (pulling group)
>>>>>>>> pull_group3_name        = chain_A17    (reference also immobile)
>>>>>>>> pull_group4_name        = chain_B26    (pulling)
>>>>>>>> pull_coord1_type        = umbrella      ; harmonic biasing force
>>>>>>>> pull_coord1_geometry    = distance      ; simple distance increase
>>>>>>>> pull_coord1_groups      = 1 2
>>>>>>>> pull_coord1_dim         = N N Y
>>>>>>>> pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm
>>>>>>>> per 1
>>>>>>>> ns
>>>>>>>> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
>>>>>>>> pull_coord1_start       = yes           ; define initial COM
>>>>>>>> distance
>>>>>>>>
>>>>>>>>> 0
>>>>>>>>>
>>>>>>>> In above protocol I want to make two reference group  as
>>>>>>>> 1-chain_A8   2- chain_A17
>>>>>>>> and two pull group.
>>>>>>>> 1- chain_B35  2- chain_B26
>>>>>>>>
>>>>>>>> You've defined four groups but then only used two, so you only get
>>>>>>>> the
>>>>>>>>
>>>>>>> effect of one reaction coordinate.
>>>>>>>
>>>>>>> What you need to do is define the pull settings for all reaction
>>>>>>> coordinates simultaneously, e.g.:
>>>>>>>
>>>>>>> pull                    = yes
>>>>>>> pull_ngroups            = 4
>>>>>>> pull_ncoords            = 2
>>>>>>> pull_group1_name        = chain_A8
>>>>>>> pull_group2_name        = chain_B35
>>>>>>> pull_group3_name        = chain_A17
>>>>>>> pull_group4_name        = chain_B26
>>>>>>> ; definition of reaction coordinate 1, groups 1-2
>>>>>>> pull_coord1_type        = umbrella
>>>>>>> pull_coord1_geometry    = distance
>>>>>>> pull_coord1_groups      = 1 2
>>>>>>> pull_coord1_dim         = N N Y
>>>>>>> pull_coord1_rate        = 0.01
>>>>>>> pull_coord1_k           = 1000
>>>>>>> pull_coord1_start       = yes
>>>>>>> ; definition of reaction coordinate 2, groups 3-4
>>>>>>> pull_coord2_type        = umbrella
>>>>>>> pull_coord2_geometry    = distance
>>>>>>> pull_coord2_groups      = 3 4
>>>>>>> pull_coord2_dim         = N N Y
>>>>>>> pull_coord2_rate        = 0.01
>>>>>>> pull_coord2_k           = 1000
>>>>>>> pull_coord2_start       = yes
>>>>>>>
>>>>>>> Note that above I changed pull_ncoords to be set to 2, because you
>>>>>>> want
>>>>>>> two reaction coordinates. Then just specify the sett
>>>>>>> +the+sett&entry=gmail&source=g>ings
>>>>>>>
>>>>>>> for each one,
>>>>>>> calling the appropriate groups by their assigned numbers.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>> Assistant Professor
>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>
>>>>>>> 303 Engel Hall
>>>>>>> 340 West Campus Dr.
>>>>>>> Blacksburg, VA 24061
>>>>>>>
>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>>>>
>>>>>>> ==================================================
>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
>>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>>
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>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>> * Rakesh Kumar Mishra*
>>>>>> *  (RA)CSD  SINP Kolkata, India*
>>>>>>
>>>>>> *E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
>>>>>>
>>>>>> *Phone n. +91 9473662491 <094736%2062491>, +91877749632*
>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> * Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
>
> *Phone n. +91 9473662491, +91877749632*
>

--
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +91877749632*
```