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 - 05:30:02 PDT
