[gmx-users] Re: Peptide folding simulation

simula_460 bharat.85.monu at gmail.com
Wed Jul 18 05:24:07 CEST 2012


I tried again simulating the same peptide with OPLS FF for 2000 ns time
duration. I used VMD for the secondary structure analysis and trajectory
visualization. This time I was able to get folding events but the residues
that are should be beta strands were helical for most of the time during
simulation. Is it because of the parameters or what else could have gone
wrong ??


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