Dear Mark, I think things are not under solution.
Please tell me if there is dsDNA of chain A (12 bp) and complimentary strand B(12 bp) like chain A- 3' - 5' chain B- 5' - 3' I am pulling 5' end of strand A and made 5' of B as a reference group along the helical direction under constant velocity pulling. And both the chains are free ( no restraint) , under this situation will the 5' of chain B (act as reference group) feel the equal and opposite force like 5' end of chain A where pulling is applied . Due to this equal and opposite force both the strand will move opposite to each other or not . On Mon, Sep 3, 2018 at 10:00 AM, Rakesh Mishra <rockin...@gmail.com> wrote: > Hi Mark > > Did you get the point or not . > Hoping your response > > On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra <rockin...@gmail.com> > wrote: > >> >> *Please remember (its your query to me )* >> 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 >> > <https://maps.google.com/?q=le+for+the+time+period+of+(t1%2B >> dt)+-+t2,+e&entry=gmail&source=g >> <https://maps.google.com/?q=le+for+the+time+period+of+%28t1%2Bdt%29+-+t2,+e&entry=gmail&source=g> >> > >> >> >> >> *This is our response * >> >> >> 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 Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra <rockin...@gmail.com> >> wrote: >> >>> Dear mark >>> I had already discussed regarding force/extension protocol. >>> But I didn't get any response from your side. I dont have >>> idea to upload some pictures. >>> >>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham <mark.j.abra...@gmail.com> >>> wrote: >>> >>>> Hi, >>>> >>>> The list cannot accept attachments. Upload to a file sharing service and >>>> share a link. We will likely need more background information also. >>>> >>>> Mark >>>> >>>> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra <rockin...@gmail.com> wrote: >>>> >>>> > Hi every body >>>> > can any one explain what is the mean of this graph >>>> > obtained from gromacs constant velocity pulling of dsDNA >>>> > along the helical direction. (force.xvg). Basically sudden drop of >>>> force >>>> > represents what ? >>>> > -- >>>> > 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-requ...@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-requ...@gromacs.org. >>>> >>> >>> >>> >>> -- >>> >>> *With Best-Rakesh Kumar Mishra* >>> * (RA)CSD SINP Kolkata, India* >>> >>> *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * >>> >>> *Phone n. +91 9473662491, +918777496532* >>> >> >> >> >> -- >> >> *With Best-Rakesh Kumar Mishra* >> * (RA)CSD SINP Kolkata, India* >> >> *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * >> >> *Phone n. +91 9473662491, +918777496532* >> > > > > -- > > *With Best-Rakesh Kumar Mishra* > * (RA)CSD SINP Kolkata, India* > > *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * > > *Phone n. +91 9473662491, +918777496532* > -- *With Best-Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@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? 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