Hi, If you want to see whether a helix forms in a given solution, start from a random coil in that solution. Don't start from a helix in another solution.
Marm On Sat, Jul 21, 2018, 17:41 Soham Sarkar <soham9...@gmail.com> wrote: > Dear Mark, > I cant properly get your reply.. If you could elaborate it, it would be > nice > - Soham > > On Sat, 21 Jul 2018, 8:47 pm Mark Abraham, <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Then all you need is the starting point for potential helix formation. > You > > don't need to see it unravel. > > > > Mark > > > > On Sat, Jul 21, 2018, 05:11 Soham Sarkar <soham9...@gmail.com> wrote: > > > > > I want to see the helix transition.. whether it is coming back or not > in > > > the presence of the protecting osmolyte where urea is already there in > > the > > > system > > > > > > On Sat, 21 Jul 2018, 2:21 am Mark Abraham, <mark.j.abra...@gmail.com> > > > wrote: > > > > > > > Hi, > > > > > > > > You haven't answered the question clearly. Do you care about > observing > > > the > > > > transition (whose properties will depend on how you introduce the > > > mixing), > > > > or just the difference between before and after? Your proposed method > > is > > > > ill formed because you can't continue a simulation after > fundamentally > > > > changing its composition. If you were watching a circus juggler > keeping > > > > five balls in the air, froze time and added two knives to the items > in > > > the > > > > air, it's not going to be consistent with any pattern in which a set > of > > > > five balls and two knives can be juggled. > > > > > > > > Mark > > > > > > > > > > > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar <soham9...@gmail.com> > wrote: > > > > > > > > > Dear Mark, > > > > > Sorry for late reply of your queries. Frankly speaking I am > planning > > to > > > > run > > > > > a REMD for 50ns with protein urea and water in it, then after 50ns > I > > > want > > > > > to add a protecting osmolyte into the system and want to continue > it > > > for > > > > > another 50ns REMD so that I can have the effect of the protecting > > > > osmolyte > > > > > before and after adding it into the system. My question is, what I > > have > > > > > planned is at all possible? How do I continue the simulation of > 50ns > > > for > > > > > another 50ns with a protecting osmolyte in it. Is there any > > references > > > or > > > > > commnad lines or protocols to execute this type of simulation which > > is > > > > > exclusively dedicated to the effect of a chemicals in the system. > > > > > Thanks in advance. > > > > > - Soham > > > > > > > > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, <soham9...@gmail.com> > > > wrote: > > > > > > > > > > > Dear all, > > > > > > I am planning to do a simulation where after 50ns of simulation > I > > > want > > > > > to > > > > > > add some other chemicals in the system and continue it for > another > > > > 50ns, > > > > > so > > > > > > that I can have the effect of that chemicals exclusively before > and > > > > after > > > > > > adding it to the system.Is it at all possible? If yes please tell > > me > > > > the > > > > > > protocol/ commands or give me some references where this type of > > > > > simulation > > > > > > is used. Thanks in advance. > > > > > > -Soham > > > > > > > > > > > -- > > > > > 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? 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