[gmx-users] Rupture force definition
Justin Lemkul
jalemkul at vt.edu
Thu Feb 15 14:34:34 CET 2018
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 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
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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 <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
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>
>
--
==================================================
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
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