[gmx-users] (no subject)

[Mark Abraham]

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 <soham9038 at 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.abraham at 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 <soham9038 at 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.abraham at 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 <soham9038 at 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, <soham9038 at 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
> > > > > >
> > > > > --
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