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?
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?
Thanks in advance
Kshatresh Dutta Dubey
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Received on Thu May 29 2014 - 02:00:02 PDT
