[gmx-users] Re: Peptide folding simulation

[jojartb at jgypk.u-szeged.hu]

Hi,
Check this article:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131
HTH Balazs

Quoting simula_460 <bharat.85.monu at gmail.com>:

> Hi,
>
> 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 ??
>
> ----
> BHARAT
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