[gmx-users] Rupture force definition
Rakesh Mishra
rockinbhu at gmail.com
Tue May 15 08:46:22 CEST 2018
Dear Justin,
In all the respect that you have suggested is absolutely correct.
But I have a question that just like a constant rate pulling
like - [pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm
per 1 ns ( which was from your umbrella sampling)]
Is there any formate in gromacs for the pulling for force rate like.
0.01 pn per ps/fs (rather than constant force pulling)
Cheers
On Thu, May 10, 2018 at 5:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/10/18 8:17 AM, Rakesh Mishra wrote:
>
>> Thanks to ur quick response
>>
>> Would you please shed some light on my query no. 1 about the box size.
>> Please go through that.
>>
>
> I don't know exactly what you'd like me to say. Your interpretation of
> GROMACS' requirements is correct. I don't know what other software does in
> this context. Use whatever you like, but be sure you are not violating the
> minimum image convention in whatever program you use.
>
> -Justin
>
> On Thu, May 10, 2018 at 5:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 5/10/18 1:24 AM, Rakesh Mishra wrote:
>>>
>>> Dear Justin,
>>>>
>>>> I have discussed a lot regarding the pulling of dsRNA/dsDNA using
>>>> gromacs
>>>> about your protocol. Thanks for those discussion.
>>>> 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 .
>>>>
>>>> Use whatever software you like. No one says you have to use GROMACS :)
>>>
>>> 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 .
>>>>
>>>> Forces are in pullf.xvg and the displacement is in pullx.xvg. You can
>>> easily plot force vs. distance from these two files.
>>>
>>> 3- But suppose we want get force versus stretch(extension) curve then
>>> how
>>>
>>>> to do constant force pulling like constant velocity.
>>>>
>>>> There is an option of constant force pulling you can set in the .mdp
>>> file,
>>> but it won't be useful to plot force vs. displacement/extension in this
>>> case because the force is, by definition, constant.
>>>
>>>
>>> 4- Should we use NAMD for simple force versus extension curve .
>>>>
>>>> NAMD can do this kind of simulation if you prefer, but you can certainly
>>> do it with GROMACS.
>>>
>>> -Justin
>>>
>>> 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:
>>>>>>
>>>>>> Dear Justin thanks for your advise.
>>>>>>
>>>>>>> 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 al
>>>>>>>>>>> <https://maps.google.com/?q=to+do+is+define+the+pull+settings+for+al&entry=gmail&source=g>l
>>>>>>>>>>> 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
>>>>>>>>>>> <https://maps.google.com/?q=n+coordinates.+Then+just+specify
>>>>>>>>>>> +the+sett&entry=gmail&source=g>ings
>>>>>>>>>>>
>>>>>>>>>>> for each one,
>>>>>>>>>>> calling the appropriate groups by their assigned n
>>>>>>>>>>> <https://maps.google.com/?q=he+appropriate+groups+by+their+
>>>>>>>>>>> assigned+n&entry=gmail&source=g>
>>>>>>>>>>>
>>>>>>>>>>> umbers.
>>>>>>>>>>>
>>>>>>>>>>> -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
>>>>>>>>>>>
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>>>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>>>
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>>>>>>>>>>>
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>>>>>>>>>>> -users
>>>>>>>>>>> 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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>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>> or
>>>>>>>> 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
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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, +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.thelemkullab.com
>>>
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
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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.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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--
* 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*
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