[gmx-users] about umbrella sampling

[Justin A. Lemkul]

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

-- 
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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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