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? 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.
