vidhya sankar wrote:
Dear Justin, Thank you for your immediate reply amidst of your busy
schedule
I am trying to pull one of chain of my protein
using umbrella option of gromacs (As did in your website tutorial)
After umbrella pulling i have extracted all frame of .gro from .trr
files . i am getting various .gro files.As stated in tutorial i am
using g_dist command it shows progression of COM between Chain A(Mobile
group) and Chain_B ( Reference group). i have not used the Perl script
using Distance.xvg files (Obtained as output of g_dist) Can i select
spacing for sampling.?
The above My Assumption is wright or wrong.?
You can choose the spacing in whatever manner you choose. The tutorial presents
one particular workflow that is convenient, but the same principles always apply
- generate configurations in some manner, choose the desired spacing and
configurations to which that spacing corresponds, and finally conduct the
umbrella sampling simulations.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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