[gmx-users] Rupture force definition
Justin Lemkul
jalemkul at vt.edu
Thu May 10 14:20:28 CEST 2018
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 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!
>>>>>>>>>>
>>>>>>>>>> * 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 <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
>>>>>>>
>>>>>>> * 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.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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
>> /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.
>>
>
>
--
==================================================
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
==================================================
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