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* -- 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.
