Thanks Jason for detailed explanation.
Regards
Kshatresh
On Thu, May 29, 2014 at 3:01 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, 2014-05-29 at 11:54 +0300, Kshatresh Dutta Dubey wrote:
> > Dear Users,
> >
> > I have some queries regarding Amber advance tutorial 17, umbrella
> > sampling:
> >
> > 1- In the tutorial, section 2, there are three scripts, 0-90, 93-147 and
> > 150-180 to generate several dihedral inputs for 0-180 degree. I am
> curious
> > to know whether one can generate a single script for 0-180
> straightforward.
> > What was the need for three scripts for same task if we can do in a
> single
> > script/stage?
>
> Sure, there's no problem with combining everything into the same script.
> The reason (I suspect) this wasn't done is given below.
>
> > 2- In the same script, I found that initial coordinate file for mdrun
> (for
> > pmemd.MPI) has taken randomly. For instance, for
> > prepare_runs_0-90.perl<
> http://ambermd.org/tutorials/advanced/tutorial17/files/prepare_runs_0-90.perl
> >
> > scripts,
> > initial coordinate is taken for dihedral.60, however script starts
> > simulations from dihdral.0 and similary for 'prepare_runs_93-147.perl,
> > initial coordinate is for dihedral.120 while it starts from dihedral.93
> > and for last script i.e. prepare_runs_150....., it is totally confusing
> to
> > me that why we have taken initial coordinate from 03.equil.rst?
>
> The goal here is to start each simulation with a structure in which the
> dihedral is _closest_ to the target dihedral angle you are simulating
> (that way the restraint force at the beginning is smaller). I suspect
> this is why 3 scripts were written instead of 1 -- each script starts
> with the "closest" simulation that has already been run.
>
> As for the final simulation, the tutorial states: "... while
> prepare_runs_150-180.perl runs 150 to 180 degrees using the 03_equil.rst
> (180 deg) as the starting structure." This structure is closer to each
> of the angles 150 to 180 than either the 60 degree or 120 degree
> starting structures.
>
> The alanine dipeptide modeled here is quite small, so you don't have to
> be quite as careful about seeding each window with structures that don't
> result initially in high forces (for larger structures, you could induce
> artifacts adopting this approach, so you may want to be more careful).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu May 29 2014 - 07:00:02 PDT
