[gmx-users] Hello

[Mark Abraham]

nikhil damle wrote:
> I am turning pbc =xyz as written in earlier correspondence. But in spite 
> of this when i run g_rms after simulation, my initial structure itself 
> shows ~1.5 nm rmsd.

So? You need to compare that with pre-simulation...

> So is it a problem at g_rms stage or it is the 
> problem related to PBC and really the peptide is flying off ??

Try trjconv like my link suggested.

Mark