[gmx-users] energy analysis

[Wang Zhun]

Hi,

I performed MD simulation of  a peptide(in extended conformation) in vaccum for 2 ns, and used the
resulted coiled conformation as initial structure for another 8 ns MD with same
parameters. After energy analysis, I found the initial energy of the second 8ns
MD was almost the same as the initial energy of the first 2 ns MD(about 400 kj/mol), instead of
the final energy of 2 ns MD(-110kj/mol).
Could someone explain this?

Thanks!