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
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