[gmx-users] (no subject)

[Soham Sarkar]

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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