Re: [gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Hi Prasad, You also have to reckon that the RMSD is always positive, so the average RMSD will also always be positive. It's a chi-variate. Try some thought experiments with distances, average distances and distances to an average position. Cheers, Tsjerk On Jan 10, 2008 8:09 PM, David van der S

Re: [gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Prasad Gajula wrote: Dear Dr. David, Thank you very for the reply. When i looked the energy minimized average structure it looks just fine. ?? but you did not say energy minimized... check the rmsd between average and minimized average structure as well. Maybe you want to do a clustering analy

[gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Dear Dr. David, Thank you very for the reply. When i looked the energy minimized average structure it looks just fine. ?? >>> >> I calcualted the average structure from the simulation trajectory. when >> I >> calculate the rmsd of the protein to this average sturture, it is giving >> average rmsd