Thanks Jason and Carlos for your patience! I have partly understood the
suggestions you have made.Yes i will definately follow some literature to
mine the same. Moreover as Jason have asked, sending you the part of my md
protocol file. My only query is, should i change the istep2 and ivalue1 to
some lower figure say 2000000 and 6.7 text made in bold and then slowly
increasing the rmsd in the &wt namelist to get the desired output? Do i
make some sense here. Though i completely understand from your text that
TMD wont support this large rmsd unfolding.But will it worth giving a try
again by changing the values? Please suggest!
------------------------------
/
&wt
TYPE='TGTRMSD', istep1=1, istep2=*4000000*, value1=*11.7*, value2=0.0,
/
&wt
TYPE='TGTRMSD', istep1=4000000, istep2=5000000, value1=0.0, value2=0.0,
/
&wt
type='END'
/
------------------------
On Wed, Mar 4, 2015 at 7:07 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> you might also give thought to starting from low rmsd and then moving
> toward high.... les likely to get stuck that way. either way, you'll have
> to spend time thinking about what the results really mean. I would not
> interpret them as giving you a folding "path". Look in the literature too,
> there is a long history of forcing things to fold/unfold and analyzing the
> results (though not as much recently, these approaches have fallen out of
> favor).
>
> On Wed, Mar 4, 2015 at 8:12 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> >
> > > On Mar 4, 2015, at 8:05 AM, Pallavi Mohanty <pallavipmohanty.gmail.com
> >
> > wrote:
> > >
> > > Thanks Carlos and Jason for your prompt relies!
> > > Do you mean to say that i need to change below mentioned part marked in
> > red
> > > to get the desired output?
> >
> > You are asking targeted MD to make an *enormous* change. I have no idea
> > how long it will take to fold a structure like this. I would suggest
> > looking at previous studies to see what has worked in the past, and then
> > appropriately scale it up to your problem. Even then, there is no
> > guarantee it will work.
> >
> > Also, nothing showed up as ‘red’ in my email client. Not all email
> > clients respect HTML markup (and some display it horribly). I would
> > suggest using some other approach to indicate where you changed values.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
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> >
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--
Regards,
Pallavi Mohanty
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Received on Wed Mar 04 2015 - 22:30:02 PST
