hi all I did MD studies of a dimer using NAMD and charmm forcefields.....now, in order analyze dynamic motions PCA was done using the command g_covar of GROMACS.....here i gave .trr and .pdb as input.....and selected backbone for analysis.....the output obtained were average.pdb, average.trr....etc.... after that for analysing i used g_anaeig command.....providing average.trr as input.....to get filter.pdb....(after loading it in VMD i could see the global movement very clearly...) my query is that " in a paper i read that PCA analysis does not make any sense by using reference structure.....in fact average structure is the best choice".I am confused whether what i did was correct or not...... and can anyone tell me how to use average structure in GROMACS
-- SUNITA GUPTA Member Research Team Lead Invent Technology TBIU, IIT Delhi, India Email- [EMAIL PROTECTED] Ph- +9111 26581524 (Ex-6)
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