[gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear justin
Thanks alot for your advice 


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On Thursday, August 24, 2017, 5:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:



On 8/21/17 5:25 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin
> Thank you so much for replyingAccording to the gromacs tuturial, i am trying to analyse my complex in terms of RMSD. In order to do that, first it is needed to obtain the average structure to get RMSD vs average structure . And average structure is a side product of obtaining RMSF. Is there anyway that i can calculate RMSD instead of geting RMSD vs average structure? If you want to caculate RMSD , wont you perform this way?

I normally compute RMSD vs. the equilibrated structure or vs. the 
crystal structure, not an average structure.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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