[gmx-users] Average and bfactors.pdb

[Justin Lemkul]

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

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