[gmx-users] About conformation choice for Umbrella sampling

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear justin ,  i regret inconvenience in the previous mail 

I have no experience with PLUMED; I could not comment.  I have been extremely 
busy lately.

> Instead of taking PDB based on g_dist over all frames Can  i  choose 
> various .gro files for doing umbrella sampling based on the pullf.xvg . 
> file
> In that file plot of force Vs time is available. i am selecting the PDBs 
> from  near  maxima of force time profile curve to time of major 
> structural change  .
> in my case Example ( 120ps to 380ps)
> can i use those PDBs for Umbrella sampling othewise  should i not  
> consider time for umbrella sampling?

I'm sorry, I have no clear idea what you're even trying to accomplish.

-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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