AMBER Archive (2003)

Subject: Comparative MD

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Jul 11 2003 - 08:29:02 CDT

Dear All,

Using AMBER7, we built the prmtop and prmcrd files (of a peptide) needed for a
MD run using the 'sequence' command of leap. We did it twice, both on IRIX-SGIs.
The 2 prmtop files are obviously identical but the 2 prmcrd files present some
very small differences (i.e. on the seventh digits after the decimal point).
Using these 2 sets of prmtop and prmcrd files, we ran the same MD-IGB1
protocole. The 2 MD trajectories are totally different (we follow the backbone
RMSD between a reference structure and the MD snapshots).

Are you surprised by this ?

Thank you very much, best regards, Francois