[gmx-users] force/time application for pull

Rakesh Mishra rockinbhu at gmail.com
Fri Aug 31 14:44:45 CEST 2018 

It will be useful for all  candidate including me those who don't want to
go for
calculating PMF but just want to study the stability of the
simple nucleic acid with drugs (ICL) or with protein+dsDNA or DNA aptamer
etc. during the structural transition.
Where rupture of dsDNA or unzipping of dsDNA is studied . It will be
extremely
helpful if force subroutine of loading rate (pn/fs or pn/ps ) can be
implemented in the gromacs library. That mean
like program of gromacs library, where this pulling is applied .

Thanks




On Fri, Aug 31, 2018 at 4:55 PM, Benson Muite <benson.muite at ut.ee> wrote:

> It can take time to read through papers. A title, link and a short summary
> would be helpful to understand what the benefit would be. In particular
> whether you just need information to add the functionality for your use
> case or whether enough people other would use the extra functionality you
> require.
>
>
> On 08/31/2018 12:42 PM, Rakesh Mishra wrote:
>
>> Dear Dr. Justin
>>
>> Ultimately Mark has not replied .
>> Can you please tell me what this peak is revealing.
>> hear 3' of one strand is fixed and 3' of another strand is pulled along
>> the
>> helical direction of dsDNA (12 bp). using constant velocity pulling using
>> your
>> protocol of umbrella sampling (output f/t .xvg file). (My motif is to see
>> rupture in presence and absence of drug).
>>
>> In my view sudden drop of force  corresponds to breaking of all the hbonds
>> of both strands occurs.
>> Whats your view .
>>
>> On Mon, Aug 27, 2018 at 12:24 PM, Rakesh Mishra <rockinbhu at gmail.com>
>> wrote:
>>
>> Dear Mark,
>>>
>>> There are several experiments have been done for protein and DNA
>>> unfolding.
>>> Thy  became pioneer in this field.  That is why force should apply and
>>> corresponding reaction
>>> coordinates are measured . Here Gromacs login do not allow to upload
>>> larger data.
>>> But I can mention some paper address . If get time Please go through
>>> these
>>> papers .
>>>
>>> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
>>> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>>>
>>> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
>>> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>>>
>>> That is  why I  asked about force-extension protocol.  In Umbrella
>>> sampling distance is increases linearly with the time and corresponding
>>> force experienced by the system writes .
>>>
>>> We still don't no that force/time which writes in .xvg file corresponds
>>> which formula like f= k(vt-x) or something else.
>>> There are other lot experiments regarding measurement of stability of the
>>> DNA and protein under f/x curve.
>>> One can see some theory paper also to see f/x like.
>>>
>>> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>>>
>>>
>>>
>>>
>>> Note- According to Justin one  can write that protocol. If suppose we
>>> write that protocol, then how  to apply in gromacs.
>>>
>>> There are only input .mdp files. We didn't know  where to built the force
>>> subroutine in .ff (force field ) directory. or somewhere else.
>>>
>>>
>>> Hoping for  response.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Aug 13, 2018 at 6:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>>
>>>> Can you please share a link to something that indicates why this would
>>>> be
>>>> a
>>>> good tool for modeling such experimental pulling scenarios? Making the
>>>> case
>>>> for implementing such a feature would benefit from that.
>>>>
>>>> Mark
>>>>
>>>> On Mon, Aug 13, 2018, 13:42 Rakesh Mishra <rockinbhu at gmail.com> wrote:
>>>>
>>>> Hello Mark,
>>>>>
>>>>> Thank for  your clarification. Gromacs pulling has simple protocol for
>>>>> pulling
>>>>> using umbrella sampling. Where one can only get f/t and x/t . here t is
>>>>> linearly
>>>>> increases for both cases of force and distance. That actually not full
>>>>>
>>>> fill
>>>>
>>>>> the need of
>>>>> experimental pulling.
>>>>>
>>>>>
>>>>> On Mon, Aug 13, 2018 at 3:26 PM Mark Abraham <mark.j.abraham at gmail.com
>>>>> >
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>>
>>>>>> It's possible, but there is no code written for it.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Mon, Aug 13, 2018, 12:47 Rakesh Mishra <rockinbhu at gmail.com>
>>>>>>
>>>>> wrote:
>>>>
>>>>> Dear Justin.
>>>>>>>
>>>>>>> Thanks for your kind  advise.
>>>>>>> But why don't it is not  possible to apply the constant force which
>>>>>>>
>>>>>> should
>>>>>>
>>>>>>> increases linearly (at each instant of time delta)
>>>>>>> like at
>>>>>>> t1 -f1
>>>>>>> t2-f2
>>>>>>> .
>>>>>>> .
>>>>>>> tn-fn
>>>>>>>
>>>>>>> and corresponding to that force we get extension for each increment
>>>>>>>
>>>>>> of
>>>>
>>>>> time in Gromacs. This is more relevant in order to map
>>>>>>> experimental work of unzipping or axial pulling of nucleic acid like
>>>>>>> DNA/RNA/protein.  Is it possible to build this protocol in Gromacs.
>>>>>>>
>>>>>>> On Thu, Aug 9, 2018 at 5:30 PM Justin Lemkul <jalemkul at vt.edu>
>>>>>>>
>>>>>> wrote:
>>>>
>>>>>
>>>>>>>> On 8/9/18 6:37 AM, Rakesh Mishra wrote:
>>>>>>>>
>>>>>>>>> Dear all,
>>>>>>>>>
>>>>>>>>> Can anyone shed some light as ,Is it possible to apply
>>>>>>>>>
>>>>>>>> force/time
>>>>
>>>>> for
>>>>>
>>>>>> pulling in gromacs. Means I want to pull my system in step wise
>>>>>>>>>
>>>>>>>> .
>>>>
>>>>> eg.
>>>>>
>>>>>>     0 - t1     force applied f1
>>>>>>>>>     t1+dt  to t2     force f2
>>>>>>>>>     t2+dt  to t3     force f3
>>>>>>>>>     .
>>>>>>>>>     .
>>>>>>>>>     .
>>>>>>>>>     tn-1 +dt  to tn     force fn
>>>>>>>>>    Is it possible.
>>>>>>>>>
>>>>>>>> Not in a single run. You would have to run a simulation for
>>>>>>>>
>>>>>>> interval
>>>>
>>>>> 0
>>>>>
>>>>>> -
>>>>>>
>>>>>>> dt, generate a new .tpr file for the time period of (t1+dt) - t2,
>>>>>>>>
>>>>>>> e
>>>>
>>>>> <https://maps.google.com/?q=le+for+the+time+period+of+(t1%2B
>>>>>
>>>> dt)+-+t2,+e&entry=gmail&source=g>
>>>>
>>>>> tc.
>>>>>
>>>>>> -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.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.
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> *With Best-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, +918777496532*
>>>>>>> --
>>>>>>> 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.
>>>>>>>
>>>>>>> --
>>>>>> 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.
>>>>>>
>>>>>>
>>>>> --
>>>>>
>>>>> *With Best-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, +918777496532*
>>>>> --
>>>>> 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.
>>>>>
>>>>> --
>>>> 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.
>>>>
>>>>
>>>
>>> --
>>>
>>> *With Best-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, +918777496532*
>>>
>>>
>>
>>
> --
> 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.
>



-- 

*With Best-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, +918777496532*

More information about the gromacs.org_gmx-users mailing list