[gmx-users] Rupture force definition
Rakesh Mishra
rockinbhu at gmail.com
Thu May 10 14:17:49 CEST 2018
Thanks to ur quick response
Would you please shed some light on my query no. 1 about the box size.
Please go through that.
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 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
>>>>>>>>> <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
>>>>>>>>>
>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>
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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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>>>>>> 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
>>>>
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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*
>>>
>>>
>>
>>
> --
> ==================================================
>
> 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
> /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*
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